Depending on the design of the tub filler valve – you would drill a hole through the plywood subfloor, stub a short jam piece of PVC pipe 1-1/2” to 2” ID (your supply lines will rise through the PVC pipe) then use mesh and waterproofing around the PVC pipe.

Here is the waterproofing stage of this bathroom - you can see the PVC stubbed through the floor. Each manufacturer designs their fillers/valves differently.

Which tub filler are you using? If you wanted to send me a photo I could see what you're working on and give you some suggestions.