Q: Restore from Time Machine backup after 10.11.3 downgrade to 10.10.5?

I am trying to install a purchased copy of Nikon's Capture NX2 photo editing software on my MacBook Pro Retina 2015.

I have learned that I can only install this software on a machine running up to OS X 10.10.5 (Yosemite) and that after an upgrade to El Capitan the software will still run.  (The software cannot be installed under El Capitan, confirmed by Nikon)

I made a Time Machine backup of my 10.11.3 system, downgraded to Yosemite with a fresh install from a USB boot disk, installed the Capture NX2 without difficulty. Runs fine.

Now I would like to restore everything from the Time Machine El Capitan backup, but maintain the install of the software (i.e. I don't want to overwrite the whole disk). Yosemite won't let me restore from the El Capitan Time Machine backup (sees files, but won't allow app or Photo Library restores)

Is this even possible?  Do I have to solve this problem by having an El Capitan and a Yosemite partition on my HD?

Thanks in advance!