As amazing as this extension is I'm sure you understand that it can not (and probably should not) try to cover every possible design subtlety. Remembering the awesome number of options could become a deterrent to use by some. Inevitably, some of the detail will have to be added by the user. So I agree with Charlie_V with regard to presets.
I also agree that adding "beta" to the title would be a very useful "warning" to alert potential users to expect changes.
Many years ago I wrote a very large program to model the operational flow of work in our facility to arrive at a price to charge the customer. We provided support to the processing and testing of satellites prior to launch. It was a "masterpiece" that covered a massive amount of the detail needed to configure the support equipment, how much of the facility and support equipment would be used, the manpower required, the days/hours involved in each portion of the process, etc. It worked great until I started adding more and more options based on what the customer might need and the manpower and equipment required to respond to them. It ultimately failed to be used when even I could not be sure all the applicable values were accounted for. Once I reverted back to the basic (but still complex) model and separately dealt with the "one-off" mission unique variations, all was well again.
Your breaking down of some of the options into separate toolbars is a great idea and is a significant help in reducing the number of things that need to be remembered.
Personally, I don't mind the flow of revisions. I find it exciting to see and try them even though I will most likely never have occasion to use them. I still think it would be easier for me to manage them if you added the revision number to the rbz file (e.g., medeek_wall_ext 0-8-1c.rbz).