What I mean is - let's suppose you have room A with an instances layer and a background layer, and room B with a tiles layer and a background layer. Both instances layer in room A and tiles layer in room B will have the same depth, so loading room B into room A will mix the tiles into the instance layer (which is what you seem to be seeing). If you are confident that you aren't mixing things into the same layer/depth, please send me a sample project where this happens and I'll take a look.
Command-line argument thing is an oversight on my part, I'll upload a new version the next few days. If you need it sooner, send me an email from your purchase email, and I'll email you the updated packer executable alone
Drag and drop import definitely still works. Are you dropping it onto workspace area (rather than onto resource tree, an editor, etc.)? IIRC there was a bug where some users couldn't drag and drop anything onto GMS2, but I thought that was fixed