This idea is doable. Emacs looks for comp-native-version-dir in native-comp-eln-load-path. comp-native-version-dir is different for different Emacsen. comp-native-version-dir consists of version and Vcomp_abi_hash. However, we can patch Vcomp_abi_hash (Vsystem_configuration and Vsystem_configuration_options) to make sure it is unchanged.
I am not sure if it is a good idea though. Upstream must have a reason to put Vsystem_configuration and Vsystem_configuration_options into consideration.