How to repair large holes in 1920's bathoom wall tiles

We are having work done to upgrade the galvanized water supply pipes in our 1916 house. Direct access is through a closet wall behind the plumbing. The current configuration for the shower wall is (top down) shower head, two cross handles set 10 inchs apart for shower), another set of handles, and an overflow that is actually the bath faucet. The new configuration will eliminate the upper two handles and add an actual bath faucet with diverter. This leaves two holes in the tiles where the upper handles were. Replacing the tiles is not an option for many reasons. Auto body Bondo has been suggested, and I've considered a painted wood shampoo shelf attached through the holes. Any better ideas would be appreciated.

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