I work in multiple workspaces with custom terminology and I receive email digests/notifications. Emails regarding a particular workspace should use the custom terminology related to the workspace I'm receiving the email notification about. The header in the digest emails (and potentially other types of emails as well) has the custom terminology from the last workspace I was in (Custom Term 1 in the screenshot), and the description of the updates has the terminology from the workspace that the record was in (Custom Term 2 in the screenshot).
This also applies to the content about linked records showing up in the digest. For example the custom terminology for the goal record, etc.