I just want to clarify first that whether you have Cornerstone activated or deactivated, since you're not using it, it won't have any performance impact on your site. The P3 Plugin Profiler does not tell the whole story. The fact is, Cornerstone outputs styles and scripts only if it is needed. Since you're not using it, no element styles and scripts will be loaded.
But, as @Prasant said, it is required by X because of shared resources like the mobile navigation. It won't work if you deactivate Cornerstone.
Regarding the WooCommerce and BuddyPress folders, like Cornerstone, they will not degrade the performance of your site. No styles, scripts and functions will be used if WooCommerce and BuddyPress aren't installed.
We understand that you are concerned of your site's speed but there's nothing to be afraid of really. What you need to look at is your site's front-end.
Regarding performance, optimization plugins like W3 Total Cache are not complete solutions. They sure are a significant help but you need a lot more like integrating a CDN, compressing your images, lazy loading content, etc..
Please also note that our performance guide is only a general guide. You should not take it as a specific solution for your site as website optimization varies from site to site. If the suggestions don't work out for you, you will need to consult with a third party developer as we do not have website optimization support. That work is quite involved.
If you wish to proceed with deactivating Cornerstone, deleting the WooCommerce and BuddyPress folders, and ask for custom code, you would need to consult with a third party developer as we do not support such modifications to the theme.
Thank you for understanding.