It would have to remount / as writable and such. I would really advise against doing anything like that in such an ad-hoc fashion, especially during bootup when you're not 100% sure the power is going to be stable. i.e. when I start my engine the voltage dips enough for the player to restart. And for various things like telnetd you'd still need to create devices in /dev etc.

It is far better to have a script on f.i. /drive0 that can be run which 'restores' all local hacks and run it from the serial console after upgrading.

Something trivial like
rw ; mkdir -p /programs0 ; mount -text2 /dev/hda /programs0 ; /programs0/setup.sh ; ro

And have all the customized things run from setup.sh.

On the other hand, allowing applications that don't really need to have a specific location to live in f.i. /drive0/usr/bin and have an /sbin/hijack (preinit) that can start executables without requiring a shell (requiring a developer image) will make installations somewhat easier.