@fariazz that’s the default behavior.
We don’t process the checkout page for compatibility reasons.
The logged in pages are also disabled by default, for the same reason.
Merging scripts and doing speed optimization very often triggers errors and stuff doesn’t always work on the frontend without changes, especially javascript.
We don’t want to let people install the plugin, not knowing how it works or how to configure it, and then complain later that they don’t have any sales because the checkout page is not working as it should.
Even if you are a developer, we don’t know if in the future you or your client is going to add some other plugin that changes the checkout page, and may break due to merging and minification.
In addition, many people use page editors which means, when they edit pages using those, javascript will again cause issues (merging should be disabled).
You can forcefully disable FVM deactivation for logged in users by disabling the fix page editors option, but make sure everything works and that you know what you are doing.