I got the following topology:
EX4300 --> QFX --> MX router.
With 1 mstp region running between all of them. MX being the root.
I noticed that on the QFX, my ae50 which goes towards the MX, was not in trunk mode. And mstp wasn't working. EX4300 keeps seeing QFX as the root and QFX keeps seeing itself as the root.
Then I enabled trunking on ae50 and vola, MSTP works and MX is the root and EX4300 and QFX also agrees.
But then I took of trunking on ae50, expecting the mstp to stop working. But as I tested it mstp still worked.
I don't understand what's trunking has to do with MSTP.