Disclaimer: Not gotten my Glowforge yet, but have had issues already while prepping some files for when it arrives. Here is my knee-jerk response to your issue.
When confronted with a smashed together file that you feel may confuse the GF UI, I would suggest to ‘select all’ in current art program, then ‘explode or ungroup’ it with whatever mechanic is available.
Then you can select each object as an individual and put some separation on them for a more definitive cut.
(not sure it would be an extended time since the GF would be doing double cuts if mushed together anyway?)
Wasted material would be insignificant and would also avoid the double cut excessive burn issues.
Try one of these formats and see if it works better for you.
PullApart.zip (10.3 KB)