I guess you’re looking for anything that can play 30 minutes of samples/tracks and has MIDI. You probably want to have one of them send both clock and transport to the other, so they start at the same time and then remain in sync.
There are lots of choices… My first choice would be the Octatrack, but I’m an Octatrack junkie, so that’s my first choice for almost anything 
I know you mentioned the OT is too large, but I think it would work well, because you can use static machines for playing longer tracks and they’ll work in stereo. There’s also time stretching on the OT — one might argue it’s not the best time stretching, but it works if you’re not trying to stretch very different tempos.
I think CDJs could be cool, but I think you might need a laptop or some other MIDI host involved. I’m pretty sure they use MIDI over USB, so you can’t use that directly with the Syntakt. If you’re using a laptop, then no need for CDJs, because you could just use software, but it would be technically possible.
- I have digitakt. seems like it’s possible to split the song into segments but it’s a very uncomfortable workflow.
I agree. Plus you’ll lose stereo if there’s stereo in the original tracks.
I think a 1010 Blackbox would work as well, but I’ve never used one myself. Maybe dig through this thread or ask your question in there: 1010music Blackbox