Incidentally, I just had some PCBs delivered 5 minutes ago where I've done something similar on a little 2-layer board.
What I did was to edit a custom WROOM footprint where I've removed the pad entirely (ie. There's soldermask where that pin will be on the WROOM, so it won't be soldered to the board at all).
What I did a while back was to rearrange the bottom pads of a WROOM footprint to make my own WROVER footprint. Back then I couldn't find WROVER EAGLE parts library. I guess it should be easier to find them now. I still want to keep consistency among my "technologies" so I'm not deleting the pads. Plus, symmetric is best for reflow and strength. In my pin usage document, I've marked off the NC pins as used on psram so I won't use them on WROOM by accident and can't migrate to a WROVER
I find the WROVER design better for routing since the once closed off bottom edge is now open and I can now route through this side.