What can I do when the rough in hole in my concrete is too large for my toilet flange?
Pour concrete (or mortar mix) to fill the space and embed your bolts into.
Wrap or otherwise protect the pipe. The UPC says:

312.1 ...Voids around piping passing through concrete floors on the ground shall be sealed.
312.2 Piping in connection with a plumbing system shall be so installed that piping or connections will not be subject to undue strains or stresses, and provisions shall be made for expansion, contraction, and structural settlement. No plumbing piping shall be directly embedded in concrete or masonry....
312.10 Sleeves. Sleeves shall be provided to protect piping
through concrete and masonry walls and concrete floors....