I'll answer your responses in alphabetical order.
Firstly, thanks, the practice is to figure things out and learn what works and what the limitations are. Why practice? Well, some of these things can't really be practiced consistently while playing so it's nice to refine it with the peace and quiet of the practice pitch. Also, what I've noticed about the playing on the practice pitch is that you have maximum advantage, like I explain below, in other words you are effectively allowed to do what you like i.e. controls will work largely as they should. As, I've always said PES is a game that suffers from multiple personality disorder, settings and game modes will have a bearing on the level of scripting involved. For example play a competitive game online Vs a game offline on easy and you'll see two completely different games, and I'm not just talking about difficulty, I'm talking consistency of controls, passes, shots, pathing, player movements/speed, cursor control speed, etc, etc, etc.
I stopped playing Master League a long time ago but when I played it was always fun. I think there was a forward player was called Castello or something who was amazing (if you can remember that far back) - anyway once I realized that the gameplay can often largely depended on the quality of players fielded I stopped - and it's not what you think but actually the reverse! What do I mean? Well, lets say you where to edit a player to 100 everything and then add him to a current team, lets say PSG, well this would actually upset the internal script chemistry and the result would not be that your team play better (with the new supposedly amazing recruit) but actually the opposite it would be detrimental. In other words the AI would actually gives itself more advantage and so you would find matches a little harder than before, if you haven't tested this I recommend you do, but that's not all because the edited player wouldn't even perform in accordance to the additional stats. In fact you won't see any increase over an unedited player which means that editing stats is largely pointless and if you don't believe me then I recommend doing it in a clear black and white manner, take a team and edit them to 100 everything and take another team and reduce their stats to the lowest of everything and play a game, I guarantee there will barely be a difference in fact the team with the lower stats may play better.
It's this internal interference that has been gradually killing the game and moving the game more toward interaction based around AI scripting rather than actual player skill and relative player stats/abilities.
Now onto answering your points...
A). You seem to completely miss what I'm saying. The players DO NOT ALWAYS RUN PAST THE DEFENDER, they are supposed to yes, but they don't always and they don't do it when I said earlier once the scripting kicks in.
Let me quickly explain Assisted Teammate controls so you understand what happens and how I use it. Once I execute the command to the player in front he will begin to make a forward run and as he goes in between defenders, just before offside but still with the advantage of acceleration, I will execute my through-pass/lob and I will find (when it works as it should) my pass finds the sent player in the free space ahead. Ok?
In my mind, that is where the advantage of this ability lies. Now, when the AI decides I'm not allowed to play the way I want (i.e. the scripting kicks in --> players become slower, clumsy, passes don't work/highly inconsistent, surrounding team players don't lend support, cursor doesn't work, AI defenders just take the ball no matter, strange deflections that seem to go back to AI no matter what, AI recovery in tackles superman-like, AI defenders outrunning faster attackers, etc etc etc - I have a name for when this period of play happens, I call it the 'advantage', it happens very blatantly online where your players will for a time play like shit and you are likely to concede a goal - all the basics stop working and it almost feels like a completely different game) the forward player will not run past the last defender like he should, like he normally would, no, in other words he isn't completing the necessary part of the move which makes it effective, in other words the AI is stopping you from using this ability. So if you see your sent player not run past the last defender then something is wrong because this is how the moves works. I'm not sure how you gain any advantage without him running forward to make space, in fact that would mean your forward player does nothing other than maintain his forward run which keeps him behind the defender, how would this create any difference? Or offer you anything different in attack? It doesn't which is why I said your understanding is completely redundant.
B). Of course it does, it's the AI :S Regarding real life players they train to time their runs yes 100% but when you are running forward at full tilt as a player it's hard to know in real time if you are offside - I play as a forward in an amateur league trust me I know, I'm usually looking at other things ^^.
C). When I said other times I'm talking about attacking play outside of using team mate controls. I find while playing my players will often make runs just offside during normal play (this is often down to subtle scripting i.e. delayed passing, but I wont go into that right now) so why would they do this given what you said about them being smart enough to stay onside during the assisted team mate control move (which doesn't actually make sense given that running ahead of the defender is what makes the 'assisted team mate control' move effective).
D). I've tested manual versus the others, it's an utter placebo in terms of believing you gain more pathing, you simply don't. PES has a fixed amount of pathing, it's has some serious limitations, if you don't know this I recommend more time on the training pitch. However, in PES2020 during the right situations (you have to remember that I said this game suffers from split personality) you may see some passes that were not available in other games however there is still a great deal of limitation in terms of pathing so the game isn't evolving as much as people think it's just the passing/shooting in general is fed through an algorithm which decides from a fixed and limited number of available passes/shots which one you are going to get and this is determined by the scripting situation, so if the advantage against you is heavy you find will your shots/passes short, linear, and perhaps off a little. Whereas repeat that all things equal but this time YOU have the scripting advantage and you'll see a pass/shot more in line with what you had envisioned, it may even seem new or unique - the higher the advantage level the more new and unique the shot/pass but the pool from which this is drawn is fixed and, which is the main problem for me, you have no control over the consistency. So you might think one time "WOW did you see that pass I did", then two seconds later all things equal you do something completely different, something worse - so there is no consistency. But hey, and a lot of people do, you could argue "but that's football" and it would be a fair point, but this isn't football, it's a computer game and skill should govern not the AI, your mistakes and plays should be your own but that's not how this game works, and it's done in a very subtle way. Going back to the previous point though about saying that the random nature happens in football, the problem with how it's done in PES is that it's not random but carefully controlled by the AI so you'll see patterns emerge in this 'randomness' and thats where the game really falls down.
P.S. This is probably the most realistic looking and feeling PES ever made but it's also the most scripting and the one where you have the least amount of real control.