Interesting proposal, but one that is not currently possible in QIIME 2.
For now you either need to run the commands one-by-one or just make sure that your sample metadata describes all samples found in your feature table (even if those samples just contain null values for all fields). After all, dropping samples missing in the metadata is all that flag does, and is something that should be easily addressed at the user end anyway:
--p-ignore-missing-samples / --p-no-ignore-missing-samples
This will suppress the error raised when the
coordinates matrix contains samples that are
not present in the metadata. Samples without
metadata are included by setting all
metadata values to: "This sample has no
metadata". This flag is only applied if at
least one sample is present in both the
coordinates matrix and the metadata.