Not a clear or easy answer here Doc. Usually it would make no difference but that is > IF another 3rd party add-on scenery is for a totally different area or coverage location other than RTMM or anywhere else that you already have add-on scenery installed depending on the scenery and where it is supposed to be placed in the scenery order.
Now it gets real interesting when you have more than one add-on scenery for a single area or the same location that is within coverage of another sceneries location, airport, or area that you already have installed: (IE: Two sceneries for the same area or airport), then regardless of "over or under" they MAY conflict and reversing "Over or under" make no difference - they will still conflict!!.
In these cases, you have to look at the location with both sceneries. Two or more sceneries for an area might actually compliment each other but more often than not they will probably conflict in one way or another (IE: overlapping buildings, or elevation issues) land covered by water or vise versa so there is no clear "blanket" answer until you test these duplicate sceneries that cover a single area/location if you have any in your system.
Now if you don't have any duplicate scenery, then the easy answer is really doesn't matter (as long as 3rd party addon scenery entries are above FTX (with a few exceptions- IE: Some of the FSAddons) and a few others) - Not exactly clear as mud - but others might have opinion on this so please chime in.