Can I switch magnet regions during a transition timeline?

You cannot begin a new transition while the playback position is traversing a transition timeline. This is a technical limitation born of the fact that a transition timeline works by allowing three separate versions of an event instance’s timeline to exist simultaneously; to support transitioning within a transition timeline, the number of simultaneous timelines (and thus the resource cost of an event instance) would be increased substantially.

Not while using magnet regions. If you’re able to switch from magnet regions to transition regions and destination regions, you might be able to work around this limitation by recreate the contents of your transition timelines on a distant section of the main timeline, and transition to that section of the timeline whenever a transition would occur instead of using a transition timeline.