AV1 is most expected to be used inside webm, though mkv can also package it.
webm is just a subset of MKV. They limited the codecs/options so that it would be easier have complete webm compatibility. (Whereas "full" MKV compatibility doesn't really make sense because it has ~infinite codecs you would need to support)
Furthermore webm/Matroska AV1 mapping isn't finalized, same situation with MP4.