do all map transitions occur as beam ins or is there a way to change that?

I think the way it is handled by the engine is this: If you go from space to ground/interior or from ground/interior to space a beam effect will occur. If you're going from ground/interor to ground/interior then no beam effect will occur.

This seems to be hardcoded. I really hope Cryptic will change that, though, and gives us a drop box (or something) in the transition element on the storyboard.

I´d like to ask, if it is possible to create map transitions without a task? I´d like to create a Starbase interior. Unfortunally I need differnt maps for that. I´d like that the player should be able to move from map to map free, without a special task in the story.

Unfortunately, as far as I can see, no. The map requires an objective to create a transition box inside the storyboard.

However, I usually greate a reach marker right where the spawn point is as the first objective of a map.
An additional benefit of this is, you can move objects more easily around the storyboard without breaking something.