The latest versions of the authoring tool (AAT) allow for editing some of the visual properties of themes. Please note that you have to be using a theme that has been coded for this capability. This feature was added in May 2019. The CHANGELOG.md notes which versions of the Vanilla theme must be used with a couple of AAT/FW combinations. Check it out. This ability can take you quite far.

Why aren't more themes available? I'm guessing that a big reason is that themes are frequently developed around client brands. FEDs are taking Vanilla and changing colors and font, and maybe some padding/margins. That bit's not much of an offer to the community. The next step is adding in a client logo and--oftentimes--background images that are again brand-specific. And those additions which really bring a theme to life are never going out the door. Lastly, mods are often done to plug-ins to integrate the theme. adapt-contrib-vanilla/less/plugins contains theme modifications for 18 plugins. I've rarely seen courses that have used all those. But a theme offered to the community ought to have these all worked out. That can be a bit of work. 

As a freelancer who does a lot of FED work, it doesn't surprise me that few themes have been offered back to the community. It takes a lot of work to strip out branding and have something left that is significantly different from Vanilla. And it takes a lot of work to produce a community-worthy theme from scratch. While I have theme ideas myself, I haven't yet found the extra (no compensation) time to create them. Kudos to those that have. Hopefully more will.

My dream is for more menus. Menus have the ability to bring a lot of personality to a course. Give me art direction for a menu, and I'm happy to modify Vanilla to extend the menu's style throughout the course. Modifying menus (adapt-contrib-boxMenu) often requires more knowledge of Adapt code than modifying the theme. Responsiveness (desktop, tablet, phone) needs to be accounted for--and hopefully accessibility and RTL, too. Many folks who use the authoring tool don't have the programming skills to modify significantly a menu.

• If you are piecing together a theme by adjusting colors and padding a little at a time, and if those adjustments don't involve the order and layout of the html divs, you don't need to develop the theme in the stand-alone framework. 
• If you have been provided art direction (PSDs for example), I'd advise you to modify Vanilla in the framework, give it a unique name, and upload to the AAT. I think you'll work more effectively/quickly in the FW.
• If you hope to reuse a theme for another course, you would do well to create an uniquely named theme. Currently, the AAT doesn't allow you to duplicate and rename themes, so create and package your unique theme in the FW.

Hope some of this was helpful.

I'd add that some basic knowledge of CSS can go a long way in cutomising the Vanilla theme. This is a great way to change the look and feel of a course. For styles you hope to use again for future courses, the additional styling can be fed into the Vanilla theme once you've downloaded its source files.