If somebody wants to replace a file-format plugin from the standard library with one of their own, today the most reliable way to do that is by adding all the plugins they do want to an allow-list.
A longer-term solution would be to submit the changes to the Kakoune standard library.
The longest-term solution would be to come up with an easier-to-manage way for users to select the parts of the standard library they want to use, and submit that to Kakoune.