Does the F5 WAF support transparent & reverse proxy mode on per-application basis

F5 supports reverse proxy (because on every asm there is a local traffic menu with LTM) and transparent one (using local traffic polices) but what do you mean writing "per application basis"?

look here for transparent https://support.f5.com/csp/article/K15099

ASM policy is applied on per VIP basis. So you could say, it is per application basis.