Now that we have everything ported to PHP, we should be able to run addReplyLinks on the server. This would mean that reply links would be visible instantly on page load to DT users, and could then have click handlers attached once JS loads.
We would probably need attach other parser metadata to the links, perhaps by JSON encoding the comment object in an data attribute. I think at the very least the comment ID is required.
This shouldn't affect the experience once the tool has loaded (e.g. the toolbar, switching between visual/source).
Testing should focus on ensuring the reply links appear when and where they are supposed to, and not when the tool is disabled.
We should also test that the page is updated correctly after posting, and the reply tools still work for subsequent comments.
Note: we should be mindful that once the patches on this ticket are merged, the risk of issues arising from T258980 will go up.