Hi Jamie, did you ever figure out how to do this? Have been trying to figure out something like this myself as well!
I do this but not with nested programs. I create a Program in the Content channel called Parent - Content X. I use this parent program as a counter but this will never acquire any leads.
Then I create separate programs for that content in each channel and use that as the acquisition. I use tags specific to the content to tie them all together to fake "rolling" it up in RCE.
The only way to next a program inside a program is to use a program inside an engagement program and kinda hijack the statuses but I haven't really thought through how that would even work.