The problem of Gundogan and Rodri playing together before wasn't "their" problem at all, it was Pep's.
They did their jobs fine in the 4231, but the issue becomes if you play 4231 you lose an extra attacking midfielder, plus, you need BOTH of your fullbacks to overlap to stretch the pitch to then make it work (Atleast that's how 4231 has been deployed typically). Liverpool, United, off the top of my head can make this work with their players and it suits them.
Our team just doesn't play this way at all (we've done it under Mancini and Pellegrini), Pep had the wingers wide, play inside, he tried lots of things in the 4231, but the attack always looked off (defense was fine).
The other problem was that you need the 10 to score goals if your sacrificing one midfielder deeper (Gundogan) and Kevin simply wasn't scoring.
We could probably make it work now with Gundogan as the 10, Bernie next to Rodri with Cancelo coming in to recreate the 4 man midfield we have now, but Pep didn't think of that back then.