the TQFP44 is simply too large
There is also VQFN44 that might work. 0.5mm pin spacing, plus the substrate, are both a bit annoying for amateur assembly...
what about the additional pins
You don't HAVE to connect all the pins that exist. Most of the Uno-sized 1284 designs don't connect all the pins.
(Alas, this is where all the various different variations show up. Decided that you really want the second UART on D0/D1 and "Serial" connected only to USB, or similar...)