I would agree to that it doesn't make much sense to put the icon.library into an eprom and burn a new one for every update. Maybe, if it were a flash rom. Nevertheless, it has a lot of advantages to use custom ROMs with WinUAE or BlizKick or other ROM emulaters. You have shorter boot times and building a new ROM image is quite easy with Remus.
But many people are
using LoadResident or LoadModule to make these libraries reset proof. This needs an extra reset only for the cold start which is neccessary for SetPatch in any case, but it speeds up all further reboots later.
Edited:
If you don't use it then SetPatch will always try to replace the resident icon.library and workbench.library with those that can be found in the LIBS: drawer, exactly as you said (but maybe without checking the version). As a result, LoadResident calls will get useless and fail and for LoadModule calls SetPatch will just waste memory by loading these two libraries again.
To avoid this rename these libraries to prevent SetPatch from finding them in LIBS:.
ok, mfilos was a little faster
Thanks for testing, mfilos !