How to remove Bootstrap JS from standard bundles not TTW?

I started to create a Diazo theme based on version 4 of Twitter Bootstrap (hereinafter BS). What solution would be more correct to prevent conflicts between BS 3 JS modules (which is included in the standard bundle "plone" and required through stub_js_modules by "plone-logged-in") and JS of BS 4 (in my bundle):

  1. Can I during installation / activation of my theme through the generic setup handler (or something else) to set a custom configuration for bundles "plone" and "plone-logged-in" and then rebuild them according to the changed settings? (I would be very grateful if someone would share a code example that demonstrates how to apply changes to the bundle and rebuild it)

  2. Or is it for some reason, there is no way to do, and I should be through manifest.cfg completely disable mentioned standard bundles, and instead incorporate into theme bundles with identical content except the JS modules of BS 3?

Or maybe there is another way?