For problem 1: Take the cloth bento box of your choice that fits the size of the Calpac, remove the Calpac from the frame, screw the new bento into place using the Calpac screws (through the cloth bottom), and then cut the bottom out of it. Boom, nice deep and easy to access bento.
Problem 2: Not much you can do if a bike doesn't fit you. Not every bike can fit every athlete, but the IAx series come pretty close.
Problem 1: I was originally thinking I would simply replace the existing calpac with my own solution as you suggest (I was thinking of fabricating something bespoke but I do like your suggestion - very straightforward and much easier). However, Dave commented earlier in the thread that the calpac is actually bonded in place, not just screwed in and also that removing it would void the frame warranty so any solution would have to involve only removing the calpac cover and perching something on top of the existing "tray" and the protrusions for holding the original silicone cover in place. That means you can't expand the volume downwards, introduces obstacles and probably denies you the re-use of existing mounting screws. Just makes the whole idea very fiddly and compromised.
Problem 2: Yep, I think it'll fit well, simply a question of how that fit is achieved. I'd like to ability to raise the basebar and/or remove some of the armrest spacers should the need arise. The only thing stopping that is a pre-trimmed steerer which is frustrating.