Things like this should be addressed before using wavy tiles in the shower.

Ask the tile manufacturer if they make extenders for fixtures like stone manufacturers make for electrical fixtures

If they don't make anything like that how big is the gap? A few beads of caulk applications should close the gap where needed or you can get matching tile some low profile matching border and make your own and install where the fixtures go... Some tile installers have a good imagination and they can make anything blend-in.

Sorry but really bad choice for shower walls , how will you ever keep them clean. Now you need some real good pro help to make sure this shower does not leak like a sieve not matter how much caulk you use. I think the best idea now is to do what GN mentioned and use a flat tile where the fixtures go sort of like an accent strip .

I'm assuming shower head and faucet are in line? I agree with an accent strip and would take some flat tile in a color that contrasts nicely with your wavy tile and run it vertically in a strip from top to bottom where the faucet and shower head are. Similar to this:

Contemporary girls bathroom · More Info