Note that a token with scope "repo" grants full access to all repositories, including private repositories, across all organizations your user can access(however, organizations with SMAL requires an additional step).
abapGit intentionally does not provide a way to store login data across sessions. This is because SAP systems are multi-user-systems and since abapGit is mostly used by developers on shared development systems who have extensive authorizations any approach to store passwords runs the risk of getting abused. On local single user systems you can easily implement the exit mentioned above to permanently store the login data in a RFC destination. Otherwise a password manager is the recommended approach to store login data.
The secure store is encrypted at rest(on the file system). And is secure(?) if ABAP code can write to the secure store and only kernel can read(ie. the secret is never in ABAP user memory) the information. In some setups, the ABAP code also reads from the store, and if this is present in a multi-user development system, there is a possibility that anyone can read the information in the secure store.
If the information in a development system secure store is also for development systems, its not a problem, as it can only impact non-critical systems. But GitHub PATs can potentially be used to access and modify proprietary or open source code.
Using the secure store to save PATs is not secure in traditional ABAP development systems, given there is ABAP code to read from the store.
In case of leaks
If there is a possibility that a token has not been kept safe, consider it as leaked, and immediately revoke the token.
Plus inform all organizations where you have access, and perform a full audit of all commits potentially created using the token. Note that git is a multi user distributed versioning system, so without signed commits, its possible for everyone to author a commit with any email address plus rewrite any part of the git history.
Protecting users and developers
Enforcing a workflow requiring peer review, will make it impossible to do direct commits to the HEAD branch. This is not a direct solution, but limits auditing effort after a leaked token. So consider setting up,