The change here is basically the same as in D108880: Rather than looking at bitcasts, look at calls and their function type. We still need to look through bitcasts to find those calls.
The change in llvm/test/CodeGen/WebAssembly/add-prototypes-conflict.ll is due to different visitation order. add-prototypes-opaque-ptrs.ll is a copy of add-prototypes.ll with -force-opaque-pointers.
clang-format: please reformat the code