Thanks for your post.
Watching the missile fly won't be possible. These are no projectiles and don't move. They just hit the target as soon as the missile is no longer possible after the launch.
The target designator allows an area selection because it uses the blueprint item prototype - the missile will always hit the left-upper-corner of this selection.
I'll change it, so the missile will hit the center of the target selection. Controlling the explosion radius by using an area selction is not planned since there are some items for the payload bay that are used for that.
The space science pack issue is "new"... I need to see why that happens - I've already fixed that in a previous version, didn't expect the bug to come back.
Edit:
Found the problem with space science and other return_items. Will be fixed in the next version.
Edit 2:
Just released a version that fixes the positioning and the rocket returns. Also does some other things.