newer kern = new modules = bigger - you have enabled the compile for small ystems option in general settings havent you ? and modules should not be an issue as they are put in /lib/modules not as part of kernel
and you could always symlink the modules folder to your emmc in theory
Tell me, all the modules you put in /lib/modules/`uname -r` will be automatically loaded right? As long as you do the proper depmod routine etc. aswell.