Misbehaviour within folders: Heal Selection takes colors from other than the active layer in a layer group.
The problem revolves around a fault in the way the plug-ins selects the context from which it heals, I found this issue specifically when using the heal selection plug-in, but it applies to others as well.
When trying to heal on a layer inside a folder, the plug-in uses the layers outside said folder instead, see example:
Selecting an area inside the folder, 10 pixels all around inwards towards center (applies in other configurations too)
Instead reconstructing the line (or similar), it fills with content from the layer outside the folder.
I don't think this is the desired behaviour, should it be that way users must be prompted with an option to change such option (GUI example below)
Please provide more details about the steps you took. From the screenshots, it is not clear that they layer you tried to heal has a squiggly line to be healed.
When I tried to reproduce (with v 3.0.0 on GIMP3), I did not get the same result. Only that the selected portion of the squiggle in the active layer WAS changed (in a bad way, it left a gap in the middle. The example is not something the Resynthesizer is capable of doing well, but maybe it is just an example.) It did not use the red background layer.
I don't think your suggested fix is good (another choice in the dialog.) Heal Selection always works on just one layer, and it should not be getting colors from other layers. If you want something else, you must rearrange and combine layers before invoking Heal Selection.
The full Filters>Map Resynthesizer will let you synthesize from one layer into another, but only two layers.
I don't think there is an issue with the Resynthesizer being confused by "folders" i.e. "Layer Groups".
I could be wrong, but I would need more details about when it goes wrong.