I'd put a bunch of leather lotion or something similar on the problem area, both inside and outside of the boot. then bend that area back and forth with your fingers for quite a while to get the problem area extra broken in/pliable. If there is a seam anywhere there, take something hard (thick plastic or a smooth stone) and rub it back and forth to slowly decrease the topographical difference (I'm sure there's a better term, but that's all I can think of right now).
How much toe room is too much? My 4473s are on the 522 last, and have lots of toe room (1" at big toe... I think I had issues with toes getting squeezed when I sized down 0.5), but are comfortable even when walking in them all day. I'm considering getting a pair of 214s from the heritage collection in the same size, which is on the 23 last. I think it is sized similarly.
It's really not about toe room, it's about matching the wide part of your foot (generally at the ball of your foot) to match up with the widest part of the boot. Having more toe room in a pair of boots than you'd have in a pair of dress shoes is normal and intentional to allow for thick warm socks.
I'm in the same boat and I wear an 8.5 in the IRs. I wear a 9 in the Beckmans so I assumed the same would be true for the IRs, but I had to exchange them to go down to the 8.5s.