I seem to have found a solution for this issue, or at least a work around that works for me: YMMV
I've merged in the OpenWRT repo (git merge -X theirs openwrt/lede-17.01) into my OnionIoT/source repo. That built flawlessly ! :). So we're running kernel 4.4.153 now. That's nice on its own (always recommended to keep up with LTS kernel versions!).
Anyway, the SPI problem persisted. Then I removed the original Onion patch file for the spi-mt7621 module (rm ramips/patches-4.4/9999-spi-mt7621.patch) and rebuilt the image. Now we're using the unpatched mainline SPI driver. Guess what: this seems to work flawlessly! :) I'm a happy man now.
I only did some quick smoke tests, so it could be other SPI stuff breaks because of the missing patch. On the other hand, there have been some commits to the spi-mt7621 module in June, so the mainline might just be the only thing we need.