I think you get better results playing your best team in your best formation, I played a counter formation to 4-1-4-1 yesterday in the league (3-5-2 V) and struggled for an hour switching formations and as soon as a switched to 3N-4-1-2 (not a natural counter) the goals just flew in.
I kind of agree with you, there seems to be a way the engine assess the squad and then it does appraissal. Afterwards it decides whether you'll win with this formation or another...
SEASON 10 LEVEL 10
4 LEAGUE TITLES
1 CHAMPIONS LEAGUE WINNER
1 CUP CHAMPION