welcome!
the undercarriage stuff - that's not terrible. i wouldn't bother unless you're planning to drop everything and refresh bushings and mounts.
the body rust - first off, that quote does seem quite excessive. i would get a few more quotes. the rear bit under the taillight is pretty bad - when that gets ground down, there will be holes, so yes, new metal will need to be welded in there. the bits under the RF fender and under the door - it's hard to say what will be left underneath, but i imagine with that bubbling action under the fender leg there will be at least some pinholes. the fender and sideskirt would need to be removed to clean that up. not a difficult job to remove.
if the fender itself is OK, you could perhaps offer to R + R the fender, sideskirt and rear bumper for the bodyshop so that you don't have to pay them to do it.
or..... you could drive it and enjoy it as-is and not worry about it.
peter
2004 330i ZHP
2005 330iT ZHP
2010 328iT M Sport