The taxonomy filter only filters posts by the terms, no the actual taxonomy.
ACF does the same thing with anything that is missing, for example if create a field group that is located on an options page and then import that field group into a site that does not have that options page, 1) the field group will not appear anywhere and 2) when you edit that field group and edit the location rule the options page will not be listed as missing.
I’m not the developer, but I wouldn’t consider this to be a bug and find it to be expected behavior. Any location rule based on something that does not exist will need to have those things created before the field group is edited.
Are you doing this moving to a new server to move the entire site? or to recreate part of it for an unrelated site?
