Jeffrey,

Another user recently pointed out essentially the same issue:
https://www.landfx.com/community/using-multiple-option-when-placing-area-refnote-changes-internal-polyline-layer-to-lg-patt-013m.html

Currently, when placing any groundcover, any boundaries are automatically moved to the groundcover edge layer as you mention, LP-GRND-EDGE-NPLT. This also includes any interior boundaries selected with the Multiple option.
I'm not sure what the best solution will be, as there is a valid argument for always moving any boundary lines, regardless of if they are the outer or an inner boundary. We are likewise struggling with the aforementioned issue with placing Site hatches, where the same is happening, but the boundary lines are moving to the hatch layer.
I don't know if the solution is to add more layers to preferences, or options in preferences, or command line options, or to have it only move polylines that are on layer 0, but leave all others as-is.

I'll add this to the discussion, and we'll come up with something.

--J