I got this on iOS last night, played up a bit, and then got it on my Android phone this morning. The two do not seem to be linked at all, despite both being associated with the same Facebook account.
The only abnormal part of the process for me probably would be migrating to Facebook after first playing as a guest on iOS. So my process looked like this:
Download on iOS, play as a guest
Progressed through about Part 4 of Chapter 1 with the red Planewalker
In the morning, I migrated to a Facebook account from the iOS device
I downloaded on Android and logged in with the same Facebook account
The Android phone does not reflect my iOS progress at all. I started from scratch and completed the tutorial on Android just to make sure. They’re completely unconnected.
I actually opened a support ticket about this same issue. I started playing on my Galaxy Note and wanted to be able to play cross-platform on my iPad.
Here is the response that I received:
“Unfortunately, Facebook Accounts for Magic: Puzzle Quest are currently not cross-platform compatible. The developers have been informed of your request. We apologize for any inconvenience.”
So it seems cross-platform compatibility is out for now.