Let me give some context here to avoid confusion.
The Cornerstone plugin is part of the X theme ecosystem. You have the Pro theme, so you can forget about the Cornerstone plugin as it is irrelevant to this conversation.
The Pro theme and the X theme were not compatible with LearnDash in the first place, and we do not support the compatibility between two.
The problem is not from Pro and not from LearnDash, in my humble opinion. This is a conflict between the two, and the underlying reason is the incompatible versions of the ReactJs library, which is used on both products.
The Pro theme is heavily dependant on the ReactJs library for the builder, and I don't think we will be able to change that for the reason of being compatible with the LearnDash plugin. I also believe that the LearnDash plugin developer won't change their version of the ReactJs, but worths the try and ask them.
There are two major versions of Pro, 2, and 3. The conflict for builders is in version 3. If you want to use the LearnDash builder, you need to use version 2. The latest iteration of version 2 is 2.5.5, which you already mentioned that is not compatible with your shortcodes, and the front end is problematic.
The only viable solution which is honestly not that impressive is to do as follows:
- Install a maintenance mode plugin that you can activate whenever you want to use the LearnDash Builder.
- Switch the theme from Pro to another one. I suggest a simple one, such as Twenty Sixteen. Please do not use old/new versions of Pro as it might cause a whole lot of other problems.
- Do the change in the LearnDash Builder while the theme is not Pro.
- Switch back to Pro.
- Disable the Maintenance plugin.
You can use our Under Construction bundled plugin for the maintenance mode purposes.
I know this will be a time-consuming way to use the theme, but honestly, I don't see any other way to go about using the incompatible LearnDash and Pro together.
I do advise against having both versions on the Pro while you have heavy customization of the Child Theme.
If you want to add a ticket for LearnDash, just inform them that their version of the ReactJs library is not compatible with the Pro theme builder ReactJs library version.
Thank you for your understanding.