Merging papers is a very tricky issue (although on the surface it looks simple).
Imagine you're merging paper down onto thick paint. The result should look as it did before the merge, which means you should be able to see the bump of the paint below through the resulting colour/paper merge.
No consider the case where you merge semi-transparent paper down onto a transparent layer below that has some opaque paint on it.
There isn't a way to produce a paper colour that can interact with the paint on the layer below to keep the result looking the same as before the merge.
What ArtRage does is try to keep the paper colour where possible (generally if you're merging down to the bottom layer, and have no visible paper on layers above, ArtRage can keep the bottom paper colour).
But where it isn't possible, ArtRage converts the paper colour into paint, and applies that to a transparent paper.
At least that way you're guaranteed to get a result that looks as close as possible to the pre-merge painting. The down-side is that you can now erase the resulting paint from the merged layer, where there would have been only paper before.
So yes, after a merge if you're merging onto paper colour above the base layer, you may very well end up with paper colour that can be erased through to transparent.
AndyRage's mantra for graphics engine code:
"Sure - how hard can it be?"