I'm unable to respond to your deeper comment, but I don't see any issue at all with this. Your concern about the vias doesn't make sense as you just tent the vi

I'm unable to respond to your deeper comment, but I don't see any issue at all with this. Your concern about the vias doesn't make sense as you just tent the vias anywhere you are concerned about shorts. I'm 100% certain you can fit both chips, all passives, etc, in this formfactor. If the flash size is a concern, RP2350 (the new version of the 2040) has integrated flash for some of their packages. Or just use a chip scale (or similar) flash instead of the one normally used on RP2040 designs.