No, GCC and clang are fully ABI compatible (modulo bugs of course). Libstc++ and libc++ are not, so use whatever is the standard library of your platform (i.e the default for calng and GCC) and things work fine.
Yes, gcc and clang use the same platform API so if they use the same headers (libstc++ or libc++) then they will indeed use identical structure layout etc.
I meant a "gcc-native" toolchain (gcc + libstdc++) vs "llvm native" (clang++ + libc++) having different layout (and there is even some interoperability between them thanks to work by the llvm team). I realize my need to do this (to try to minimize opting bugs) is a special case, and probably unusual.
There is not really anything more “native” about using libc++ with clang as opposed to libstdc++ other than the fact that they happened to be developed by the same project. Using clang with libstdc++ is extremely mainstream and normal.
Actually I would bet that even among clang users, libstdc++ is used more commonly on GNU/Linux (IDK for sure, but it’s my hunch).