@Wile_E_Coyote: close, but the twist is not in the ROOT libs, assuming no AVX-specific implementation details are exposed (e.g. different memory layout for classes with or without AVX as is the case with Eigen as also exemplified in the other topic). The real issue is with the PCMs/PCH (incl. I/O dictionaries). Since for Clang part of the AVX implementation consists of header files, if -mavx is not used when building the PCMs/PCH, __AVX__ will be undefined and no amount of compiler flags allows enabling AVX from that point on. (The reverse is also true.)
Normal use of cppyy gets away with looking at CPU features b/c the PCH is (re)build after installation or on first use. In the case of ROOT, the first half of that feature is kept, but the other half is gone. Hence fun ensues.