I also have a pretty similar system and the short answer is no imho.... 4,1 flashed to 5,1 Mac Pro with 3 HD spinners and one SSD. ... If I take out the 3 spinner drives and only leave the SSD for a clean install, will High Sierra still convert the 3 HD spinners to the new file system after the High Sierra installation has already completed? What if I have a second SSD with El Capitan on it and I want to use it along with High Sierra, will High Sierra convert this 2nd SSD to new file system or leave it alone?Similar situation and would like to know the answer too.
Installing HS by running the full 17A365 installer only touched the target SSD. I have two more SSDs in my 4,1/5,1 one running El Cap, and another with Yosemite and Mavericks on two partitions. These weren't converted to APSF.
Granted, I've left my three spinners in place. However I doubt that the HS installer automatically converts anything else than the startup SSD in a cMP.
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