In XP2 the org.wildfly.bootable-jar module is in system/layers/base, making it an outlier as the only module XP installs that isn't put in system/layers/microprofile.

There's no advantage to doing this. Even if at some point base EAP provided the module in 'base', if the XP FP were to also provide it, the content put down by the XP FP would take precedence. Or perhaps there'd be a mess. So long as the XP branch has java code for this it should put the module for its code in the microprofile area.