Derailleurs for indexed gears have two different jockey wheels. If you look at a derailleur that is not installed on a bike, you can move the upper jockey wheel side to side by a small margin. Lower jockey wheel does not move side to side.

I have no idea if that kit with new wheels is built that way. If not and if your jockey wheels do not allow that extra play for side to side motion, if your drive train becomes a bit noisier or if the shifting does not work well, that could be the reason.

If you have not changed them yet, you can check this on your existing setup.