I definitely agree with all this, but right now I'll prefer doing something which can be used "today" :)
Of course, feel free to begin with what suits you best :)
I've written a loader which loads kernel binaries from /mint/ and allows the kernel to process the remainder of the auto folder (some ugly DTA magic was needed, but it's the same ugly magic that's already in the kernel init code (init.c, get_my_name()).
Why all this hassle? Shouldn't mint.prg be the last program to execute from AUTO? (the rest should be from mint.cnf or xaaes.cnf)
#define MINTDIR "c:\\mint"
There's better way -- env variable called SYSDIR (try echo $SYSDIR in shell :)