Prerequisites (mark completed items with an [x]):

• I have checked that my issue type is not listed here https://github.com/woocommerce/woocommerce/issues/new/choose
• My issue is not a security issue, support request, bug report, enhancement or feature request (Please use the link above if it is).

Issue Description:

Despite our work in #34879 and #35063, there are a still a few other flows/places that can lead to a plugin being activated and that are currently not being observed for possible conflicts with HPOS or other features:

1. Plugins on the Plugins screen that are installed but not active.
2. Plugins > Add New. Here you can search for a plugin and click "Activate".
3. WC > Extensions > My Subscriptions which displays a toggle to activate/deactivate the subscription and, in turn, calls activate_plugin() and deactivate_plugin().
4. WCCOM remote installation feature. When you connect your site to WCCOM, purchase an extension and use the "Add to site" feature it'll not only install the extension but activate it automatically.

Given compatibility is declared via code, I'm not sure if we can fix that easily at this point. Even if we used headers or one of the other proposed solutions, only for (1) and (3) the plugin file is already in the web server and can be read. For the others the plugin information comes remotely or is handled entirely outside of WC.