Ah, this is very interesting. It does seem Krita supports merging non contiguous layers by clicking the “merge with layer below” option in the context menu. I never attempted it because the wording used “with layer below” implies ordering but this would be for a different discussion I suppose.
Now regarding :
But there’s also a number of people who deliberately and regularly use this functionality to their advantage and they should not be ignored.
I agree they should not be ignored, but there is already a way to avoid the layer being merged (by not selecting it).
The thing is, merging layers, in essence is a destructive operation as data is going to be lost no matter what and I believe Krita should not make it easy to lose data, especially not by “design”.
I may be mistaken and obviously state the following based on my own usages of Krita, but I can only think that people who expect the hidden layers to be discarded either used the hidden layers as “draft” or “references” rather as it being part of the intended final piece OR deliberately wanted to “delete” that layer.
If the former (using the hidden layer as reference) I think this should be handled by a different feature request (to support marking layers as drafts, so that they are not included in certain operations like exporting and possibly merging?) or using the color labels for this purpose.
