Wasn't really bothered about 3 CB lineup.
Don't think it was a 4-4-2, or was not a flat one offensively at least. Defensively yes, because midfield stretches and fills in a 4-4-2 to cover for fullbacks who just missed a cross and then presses opponent fullback as your fullback is busy with their winger, but then it recovers from that every time. Don't understand why that would make it any weaker though. On which end? Certainly not on offense. You could argue it's weaker when playing against an organised 4-3-3 that is excellent at what they do as they'll always have numbers advantage in the middle but even then a good 4-4-2 can compete like Madrid's did. Or Atleti's from few years back, and now.
The only weaker thing theoretically is the wings offensively where fullback does just about everything and must be elite making fewest giveaways, but he has more options on each delivery too.
I really don't understand what you or Andresito for instance have against it being used the way it is now i.e. in 10% of the fixtures to find solutions when banging your head against the wall with a 4-3-3 isn't working because 90% of the team is out of form. Orthodox 4-3-3 with sodall deviation depending on select names is the worst thing you can do to a team. See Pep's blockheaded approach.
E:
Anyway, I think Madrid's current wingers being this poor against low block with so little direction from the coach and Fede/Modrić usually being the ones to break the lines calls for a 2-striker shift. We made more openings when Jović and Benzema played together. If Zidane made a habit of introducing a 2nd striker (can be Mariano as well) at 60 mins mark and letting Mendy & Carva take the sides to themselves, with maybe Odegaard at #10, it'd be infinitely easier for Madrid to break the bus down.
Problems are that Mendy isn't consistent in attack and that vets aren't invested in organising themselves in such setup with new faces. So many times Jović tries to make a run and vets don't feel like risking it. I think the one noticable time was when Benzema did a cross-field pass and Jović chested it down and Emerson(?) got sent off vs Betis tackling him. Little things like that that make a huge difference.
You could see that Madrid plays better football when it's 60-70% B team rather than the team where Ode and Odrio are slotted in. Vets are such wankers at mingling with the newbies a lot of the time and are so much more lenient of a dude like Vazquez. Unless you're smart beyond your years like Fede or Rodry, you have no chance for right direction in Madrid.