Hey all,
We do now have a way to output metadata in an artifact with the semantic type ImmutableMetadata (see 2023.5 release notes), and this can pave the way to supporting other metadata merging strategies through specific commands as @fedarko suggests.
ImmutableMetadata is viewable as qiime2.Metadata, so can be used anywhere that metadata can be in QIIME 2, and it can be exported which results in a plain, old (mutable) metadata .tsv file. ImmutableMetadata will of course have provenance associated with it, and the .tsv of course won't, so working downstream with the ImmutableMetadata artifact is preferred where possible for maintaining the provenance chain.
We also have a long-standing PR that addresses another issue: merging metadata with overlapping column names, which isn't possible right now.
Let me check in with the folks on my team and I'll follow up here with some notes on our plan for moving this forward.