Glad it worked.
BUT ...... I have 2 concerns about this method.
1. How long is it going to last? How are we going to boot up newer macs which won't support El Capitan? It's not going to work anymore, is it?
2. The need for El Capitan and partitions. This should not be necessary.
To test the second method specified in apple's developer forums I actually did something very similar for 10.12.1 beta 2, except I used an external HD instead of SSD. Yours is probably faster.
Anyway before that I tested the method out on the final GM of Sierra on the other partition to see if it really is Sierra that is the culprit here, not the partitioning. Sierra was definitely the culprit. So I wiped that and put El Capitan there instead and thereafter it worked.
But I'm still trying to find out what part of Sierra is causing the problem. Actually what I really want is some way to get the packages to install individually from within Sierra so as to eliminate the need for El Capitan and another partition.
This way it won't matter if newer macs won't support El Capitan.
The most obvious part of Sierra and El Capitan which is different is the installer.app from /System/Library/CoreServices which run the packages. They both have version number 6.2.0 ... HOWEVER .... different bundle versions 909 and 853 respectively.
So the next time there is a beta, I'll try running the packages through installer.app bundle version 853 from within Sierra and see if that helps.
If this works it will mean there is only a tiny bit of El Capitan which is needed, i.e., the installer app which you can just copy out from /System/Library/CoreServices. It's about 10MB as opposed to 6GB!
It is tempting to upload it somewhere but unfortunately it is proprietary software owned by apple. So although you can get it free by installing El Captan it would be illegal to upload it somewhere. So the only legal way to get it is copy it out from El Capitan into Sierra.
So it doesn't totally solve the problem, but may go some way towards simplifying it.