This was reported as part of a larger bug listing issues with flight plan behavior, but you're right, it should probably get filed separately as its own issue.
I'll try to remember to do that tonight.
IRL, "direct to" creates a virtual origin waypoint for the pink line, but that point doesn't appear in flight plan page. Direct-To with an already-active flight plan shows a little pink arrow next to the point you're flying to, and disactivates an already-active leg according to some logic I don't 100% understand.