Hi @Stefan,
It kind of sounds to me like you have a new FeatureData[Placement] type (or something like that). You should be able to recycle the strategy that the other merge methods use (there aren't any privileged plugins in QIIME 2, so anything that one plugin does, any other plugin can also do).
It does sound like you might benefit on waiting for variadic inputs however, which will be supported soon. Here's a recent forum post on that.