You're welcome - and thank you for giving me my first workout with 2.5!
This statement confuses me.. your post says that the HDR files have "artifacts in the highlights", and the screenshot in the issue you opened on Github shows that the grey artifacts are in the highlights of the lamps (the center of the flame of oil lamp on the desk, and the sconces on the wall.) These gray spots are caused by overexposure (specifically, the green and blue channel) in your darkest frame.
(this is what I mean here - I thought these gray areas in the sconces were what you meant by "artifacts in the highlights" - top is Darktable's raw overexposure indicator, bottom is from your post on issue 43.)
If this isn't what you mean, perhaps you could post small 100% crops of the issue?
OK; I've noticed that mismatches between the images and response mapping can cause colour banding and false colours. It looked like there was some of that in the shadows around the right window, so I thought that's what you could be talking about. Interestingly this banding also shows up when I use 2.5, but not when I use version 2.4.0, so this is definitely a bug in 2.5's HDR creation. (In fact, profile 5 - my go-to for RAWs in earlier versions - was unusable with 2.5.)
Yes, the way Luminance HDR deals with blown highlights has always bugged me. It took me awhile to understand what was causing it and how to correct it in my workflow. Unfortunately, from this first real test, it appears that there could be some regressions as well (The banding artifacts might be caused by a library on my system, I'll have to do some experimenting to see if I can track down the culprit, then file a bug report.)
I tried making a highlight reconstruction image (underexposed by 1 stop) with the rest and was able to recover some of the grey area of the sconces, but it's not perfect and would still require some retouching (as well as curve adjustment.). This is about the best I can get without more time, which I won't have for another few weeks.