It uses the 10.11 SDK but it's still compatible with 10.10 so in fact you should be fine with using 5.6 on macOS <10.10 (those Objective C++ templates are not features of the SDK but rather of the compiler and we use our own compilers that supports them just fine).
It was not possible to support Qt 5.9 on macOS 10.9. This is an upstream decision and although I spent many hours reverting these changes in the end it was a mountain I did not see an end to. I have the patches (I guess you saw them already?) if you care to continue to this battle; you'll run into the cliff face that is chromium/QtWebEngine quite quickly as that's where I threw in the towel.
Instead I have done everything in my power to make sure 5.6 is not forced upon users of PyQt and Miniconda.
The next Anaconda Distribution full installer releases will probably bundle 5.9.
An example of something that'll not work is the forthcoming RStudio 1.2 release since they've moved onto 5.9.
These last two points, coupled with the fact that Anaconda Navigator is based around Qt force our hand wrt macOS 10.9 support in the full installer. We cannot swap out Qt versions while it is running (when our users attempt to install RStudio).
It is a shame because many of the changes related to dropping 10.9 were made in the interest of code cleanliness and saving effort and they could've been done in a backwards compatible way in general.
Sorry about that. 10.9 had just fallen off the end of many an upstream's view cones (see the entire R world for another depressing examplen of this).