This should be unbundled.
No idea what tweaks people did for repeatmasker.
Hmm, I made yet another, sci-biology/ncbi-blast+ (in sci overlay).
On a general note, ncbi-blast+ is released from NCBI at higher pace than ncbi-tools++ so while at the very moment there is only blast+-2.2.28 available through ncbi-tools++ bundle there is for a long while blast+-2.2.30 through ncbi-blast+ (smaller subset, faster release procedure). So, it makes sense to provide both, even I would say to allow the smaller subset to overwrite binaries from the huge bundle (yeah, forcing static build but that's not a problem).
But the question what is different to the version from repeatmasker ... I don't know.
First the ebuilds for ncbi-tools++ and ncbi-blast+ should get polished (by you) ;-) , moved to main tree, then I would say one could think of rmblast variant.