Have you tried asking a question on the
raspberrypi.org forum in the linuxcnc thread?
I think the jessie install will definite not work on stretch, there were a few knowledgable people at rpi forum that may be able to help you if you ask, I think kinsa was the username of the guy that did the external hardware addon and he is fairly hot with kernel compiles and driver devel.
I have not used machinekit on rpi3 since just after it was released early last year, it compiled okay then for stretch and jessie and wheezy with the auto build scripts we use but there was one library that needs to be downgraded with a fairly simple source compile for stretch (I forget which one probably czmq or zmq or protobuf?)
I doubt you will get a RT_PREEMPT kernel for pi3 I think the usb patch and spinlock mods would be different and the anholt gpu driver changes some stuff, thought things may have changed, unfortunately the raspberry pi foundation do not seem to want me on their forums so we moved on to try and find other systems for cnc development (still not found any ARM sbc that is receptive though)
The pi is probably very good platform especially for the multikore stuff, but you will be on your own as far as RT and any other more complex aspects of patching and driver stuff, the rpi foundation do not seem to like more comercial usage of their devices which I suppose is understandable if they cut their profits to support education they cannot be expected to waste time and money supporting commercial product usage of a charity subsidised product.
But maybe still worth asking on their forum?