So this was because you are loading an Instances_1 layer from room0 (where it is at depth 100) into rm_test, which has an Instances_1 layer at depth 500000, thus causing them to be added to that existing layer. In other words, if you need the added layer to be at a specific depth (that's inconsistent with target room), you would have to name it differently in the to-be-imported room.
I'm not actually sure what's the right way to handle this - if I let GMRoomPack create layer(s) with the same names as existing layers in the target room (but at different depths), you could get any of the same-named ones when asking for a layer by name, which would make a far bigger mess.
Uploaded a new version that fixes packer issues though