I have a similar problem, trying to sync the MF to Ableton (as this is my brain)
Unlike my Syntakt, where I can start/stop it independently and thus creating stuff without the need for Ableton to be running, the MF does not.
I can set clock to automatic and then I'm able to use the MF without Ableton playing, but then the Arp/Seq is synced internally, which has a totally different time. I set it so to test stuff: Ableton runs at 128 and the MF at 84 so it's totally clear when what is what.
And this counts ofc for ALL synced elements on the MF