While no boat is particularly fond of hitting rocks, aluminum boats seem to fare better in the rocky, gravel and sandy bars that one is likely to encounter on the waters of SW Idaho at least. Its not uncommon to hit a few rocks just when landing a boat along the river and Fiberglas breaks, aluminum bends.
Also, you said that you would like to run "shallow" like 3 ft. In the winter there are places where my boat never sees 3ft of water in the whole channel. 3ft would be a luxury and honestly, if you don't run in anything less than 3ft, you might be ok with a fiberglass bottom.
"Remember that one time you made hot chocolate?....." Jaden