Was a bug in PKHeX.Core for D/P, and has been fixed: Gen 4/Diamond - Injected wondercards do not activate gift flag · Issue #4407 · kwsch/PKHeX
How to work around it for now? inject both the PGT and PCD. If codemonkey85 wants to add another workaround, I think setting the gifts in reverse order will allow PGT-slot0 to retain its "isActive" status.