I would keep compiler related checks into src_* functions (src_prepare for example). But ok, in the case of samba, this fits in the middle, because it also does USE flag tests.
On a side note, MERGE_TYPE is a whacky thing introduced in EAPI=4 to avoid moving all the build-time code that is in pkg_* elsewhere. Yay for not fixing things at their root. -- Fabio Erculiani