Another smart option that Pixelmator doesn't currently employ to save designers time is how the top Layer will overwrite the name of the lower one(s) that it is merged with.
I propose that if the top layer has been issued a default name e.g. "Layer 5" and the one beneath it is to be merged with has something that the user has specifically renamed e.g. "top left corner", then that non-default name should be maintained.
Of course, this will only work with two layers having been merged, and if the two of them are default names or both renamed, then the one above can overwrite as is present practice, but would be a nice little time saver.
What features would you like to see in Pixelmator?