This is not something I've tried yet, so I can't help specifically. You're running uphill by choosing formats that rarely appear out there; USB is what unetbootin thrives in.
Anyway, I found a wiki for Thinkpad / Windows CF booting. You might learn a thing or two about 10k and 100k-write durability designs, general tuning tips and even the fixed disk / removable disk issues that can translate to your purposes. The hardest part is probably going to be ensuring that current USB tools like unetbooting read your CF card. Next hardest will probably be even finding motherboards trying to even offer booting for CF.
When manufacturers fail to provide a standard and users fail to demand one (I think that's how el-torito bootable CD's and even bootable USB support came about). Your request sounds like a roll-your-own solution kind-of thing, which is hard to do unless you're a hardware hacker with means to solder things together and program new logic into chips. Good luck!