Unfortunately this system is very much so working as it's designed to. We can't leave orphaned properties for a few reasons. If you remove the add-on, and we leave the properties behind, those properties could be totally broken. Phases will no longer exist, the properties may depend on a template belonging to the add-on to even render it.
It's also potentially problematic and unexpected for the end user who installs the style and they don't have the add-on installed. Those XFRM properties will still be imported, but they'll be listed under "Ungrouped properties". To solve that problem, you might want to consider exporting your styles using the "Export from add-on" option. So you'd do an export for XF only, XFRM only, XFMG only, etc.
There's even a possible scenario whereby you could physically develop them as totally separate styles, and still do the "Export from add-on" option when exporting each one. That would likely solve the "dangerous" part you mentioned.
The individual add-on based exports can then be imported into the same style (using the overwrite option). The overwrite option will only overwrite templates and properties of the same name, it doesn't totally overwrite the entire style (at least not with the add-on export option).