Budget issues...pls advise :

can I choose to hack and lay only toilet floor tiles, and retain current wall tiles?

Will water proofing be an issue, and if so, can I just lay another water proofing membrane after hacking floor tiles to manage this issue?

Definitely can. Just ask your contractor to make sure that it will be water proof!! It doesn't cost much too if they charge you.

Yes, can do but that time when i did mine, some of the contractors will request to see your toilet before they advise you. Let them advise you, just get a few quotes to compare. My waterproofing is around $150 for the toilet, seems like a standard rate. Out of all, only 2 of the contractors have workers that undergo waterproofing certification. Just take it as a reassurance that the waterproofing is not done by random workers, by the time problems come back, the warranty is over.