Your logic beggars belief my friend and runs parallel with my "Child-Brides" logic on money - What's hers is hers and what's mine is half hers! There is no way you can have 4 minutes drawn out to 7 especially when you have kept possession to run the clock down. I was far from happy with FM10 and tried FM11 reluctantly but gave it away after 3 attempts. It's ratsh!t! I will NOT be purchasing FM12.
The problem with the FM games is that essentially the control you have over your players will always be limited. No matter how realistic they make the behind the scenes transfer dealings and the control over finances etc. The actual match will always be played based on a complex system of probabilities which you see in the form of events happening on the pitch. The tactics you give the team and everything you control will affect the numbers that go into the endless equations of probability and this will come back to you as shots, goals, etc. This system works fine with turn-based games like Final Fantasy or Pokemon etc. but with real-time games it simply cannot work. You will never be able to see a direct link between your team's failings and the tactics you're playing with. It's fun all the same, but if you try to get really into it and it starts bugging you, I'm afraid you'll never really be able to control what goes on on the pitch.
Yes you can, as described above. 4 minutes stoppages is actually a minimum of 4 minutes so can easily be nearly 5 minutes. Two goals in stoppages automatically takes it to nearly 6 minutes as referees are instructed to add 30 seconds for goals and substitutions (unless they feel time is being wasted in which case add more), and it only needs to go to 6 minutes and 0.01 seconds for them to be scoring a 97th minute goal. The restart would be near enough 6 minutes 30 into it so your match would finish deep into the 7th minute if he blew straigh away. And you can't have kept possession that well during stoppages if they're managing to score 3 goals. I don''t know what you're doing with your team instructions though, even with a 1 goal margin I rarely concede in stoppages or have the clock overrun. You usually can with the pitch views etc. Using City as an example, if their right winger keeps getting crosses in you can usually see on the pitch view that he keeps doing Dawson for pace. In response you switch Rosenior over to that side and bring on your sub right back and the problem is solved, though it might create another problem elsewhere, mainly the fact McShane is likely to be your sub right back.