I don't even understand why it's so hard to fix this.
I've looked at all the AI managed teams in the PL and it seems you are correct, they only start their first pref, Defensive or Attacking formation ( depending on the opposition ).
However there is one exception and I am bolding it. Unai Emery has 4-2-4 Wide as first pref and he is the only one using his second formation 4-2-3-1 as the starting lineup when he faces a tough team.
So.. It seems that it works only when AI's the first pref is 4-2-4.. For the others, no matter what is their first pref, 4-4-2, 4-2-3-1, 4-3-3, 5-3-2 etc... they never use their second pref no matter the opposition.
I think we can safely say... its not working as intended