Hey all! Thanks for all the great suggestions and feedback. I was actually nervous about posting this and felt it might have been taken the wrong way, but thank you all for being really helpful and starting a productive conversation. At this point, I think I have a way forward to solve these issues, broken up into individual phases.
Short term, I will be working to make the existing documentation devoid of all instructions and rather make it a descriptive reference for the config. This will help focus the current pages to cover all features of the config (along with their reasoning), rather than being a confusing and awkward mix of both instructions and reference. To replace the instructions, I will be making a new page with a step by step guide, accompanied by a GIF for each step, as well as a full video tutorial on how to install the config. The steps themselves will also be revised, removing things like the clean up step which seems to be most daunting step (also ironically the first). Next, I will be adding migration guides from Comanglia, cfg.tf and tf2mate which should cover the vast majority of config usage and similar variants.
Longer term, I will be reworking how I release the config. There will be two release channels, stable and pre. Stable will be a more tested and less frequently updated version of the config released around every month. Pre will continue the sometimes daily updates that mastercomfig currently provides, where I may test things and revert them the next day. Pre will be the default. In addition to new release channels, there will be two mastercomfig packages. One will be as it exists currently, and called auto. This will be the default. The new package being added will be manual. This one will have to be manually set up from your own configs, so you use what you want and don't have sudden breakage. All these switches will be provided on the download page, with an explanation of the differences between each, plus a link on how to install either package.
After that in the future, I will be releasing the new app. This one will have a smoother installation proccess than the previous one. Additionally, it will have a flexible and advanced scripting backend which will allow me to better manage how the app generates configs and for you to customize the entire generation process (through the app's menus or by writing code yourself). This was a problem in 7 and ultimately made it too hard to maintain.
Again, thanks so much for taking the time to share your thoughts. I really enjoyed it and hope to continue conversing with the TF2 community to keep on improving mastercomfig together. If you have any further suggestions, the discussion is completely still open so feel free! I'd love to hear your thoughts on these plans and any other remaining concerns.