Hi Ross,
Thanks for voicing your concerns! This is definitely an area which TBC can and must improve upon, especially with the new X7 Scanner hitting the market very soon.
Might I suggest implementing selection sets to your workflow to better organize data? In the view filter manager, you can turn on/off selection sets created from raw data files to give you finer control the view, as you mentioned in your post.

Merging projects would be an engineering nightmare, with all the conflicts we'd have to consider. Lessons were learned during the development of the 'Merge Survey Projects' command. I'd prefer to keep vces separate and improve our means of organizing data in a single project.
Joshua