Especially in this case, I’d say “deprecated” means “recommended against”. So there isn’t a public plan (that I know of) to make non-scoped tokens not work, but they strongly recommend you don’t use them.
We currently have a number of workloads that use API Tokens against Atlassian REST and GraphQL APIs for products which aren’t listed under the “select app” choices for Scoped Tokens.
The current apps which support scoped api tokens is limited to Bitbucket, Confluence, Jira align and Jira.