Can I just used bondo or automotive caulking fill in the little holes

I would use Porpatch. and clean and coat the underside as well. That way the repair will be permanent and not temporary! The pic also shows what look like cracks, if they are cracks, they need to be dressed and welded before you do anything else-if you cover then, they will come back.

Will

I agree on the POR Patch.

Not a bad idea to patch it now before you weld the final piece visible in the hatch area. But you might be better off waiting till AFTER you have that last piece one, and then using the POR patch. If only to avoid the nasty fumes of welding through the POR.

While caulking would help seal it, it wouldn't do as good a job as the POR Patch.

Don't use Bondo, it's not designed as an adhesive nor as a seam sealer (it's porous).

FWIW

Enrique