We are also seeing this problem on an upgraded site, but we are unclear when the problem started -- we have likely upgraded both Metatag and Search API several times before the client noticed the issue. However:
We previously had on our index, and this was used to provide heavily weighted search results on those keywords.
The field remains in our index (as does the ability to "add" a new field_metatags entry) but none of them are actually indexed based on my review of the DB and the lack of any search results.
Per the OP, we see this message when trying to add a field:
Skipped fields
The following fields cannot be indexed since there is no type mapping for them:
Layout (type "layout_section")
Metatags (type "metatag")
Metatags (Hidden field for JSON support) (type "field_item:metatag_computed")
If you think one of these fields should be available for indexing, report this in the module's issue queue. (Make sure to first search for an existing issue for this field.) Note that entity-valued fields generally can be indexed by either indexing their parent reference field, or their child entity ID field.
We are currently running the latest releases of Metatag+Search API -- based on the wording it appears this might better belong in the Metatag queue.
I landed here via Google after encountering the same error. In my case:
I'm working on a Github action to build/test the site install prior to an automated deployment. I'm running:
drush si --existing-config
to install the site from its existing configuration. My action fails due these errors and I don't believe I can really place them into /optional because I'm installing directly from our config/sync folder (not from and install profile.)