Thank you for starting this thread!
We would love to add such functionality, but I am afraid that it is not possible to have unrestricted HTML editing and drag/drop functionality at once. It is either one or the other, and I think that Bootstrap Studio has made the right choice in preferring visual editing. Our Custom Code component can go a long way in giving you full control when you need it, while retaining drag/drop and other smart features for the rest of your page.
We will make visual editing even better in the future. We released version 2.6 a few days ago that makes it easier to edit CSS, and we have a lot more planned. But being able edit the HTML outside of Custom Code would unfortunately never be possible.
The CSS commenting is an interesting suggestion. I think it won't be difficult to insert comments on top of CSS blocks, like we do for media queries at the moment. Comments in between CSS properties would be quite confusing though.