Sad part is that so many authors included them in the theme, that buyers here are actually expecting the theme shortcodes and CPTs to work as soon as the theme is installed. “It works in the demo, why the hell is my site broken when I install your theme?!” doesn’t look too good for sales… so authors keep including them.
This isn't a user problem though. It's a developer one. More specifically, it's a TF developer problem. You rarely see this type of issue in the larger WP theme developer community, and the few lingering issues are being worked out by the development community.
Too many developers here on TF are thinking about the bottom line rather than what's best for their users. When you add functionality that literally holds the key to a user's content within a theme, you're locking them into using your theme and your theme only, at least until the user hires another developer to fix your crap.
Not only is this bad development practice, it's an unethical business tactic.
Shortcodes in themes sold here are tightly bound with the theme itself. Having them in a separate plugin to be used with another theme is never going work.
This is exactly why there's such a problem on TF with these things. Rather than saying you can't do something, you should be asking, "What solutions can we come up with?" and working to fix the problem.
A developer's job is to come up with solutions for problems.
Quick example: how a tab (or column) shortcode using twitter bootstrap is supposed to work in a theme not using it ?
Any 13-year-old WP developer with Bootstrap knowledge could write this plugin in about two hours. Any more examples?
And who’s going to handle support for such situations ?
Be more specific. Each scenario has a different solution.