The reason you ran into this way-to-dark problem is because darktable isn’t all that smart when applying auto scene referred settings. Especially in this case because it could be picked up easily and resolved by darktable while parsing this RAW.
The actual problem is this: You use scene-referred, which activates and sets filmic and exposure. This does not work correctly when you shoot manual and, for whatever reason, have adjusted the exposure compensation button on your camera. darktable blindly add/subtracts the found value (+3.3 in your case), which it shouldn’t do when you use M(anual) mode because in that case is doesn’t change any of the ISO, speed or aperture settings.
It is one of the reason why I’ve set my workflow to none and do it all manually. I always shoot in manual mode, dial-in my settings using the (live) histogram. I then use the exposure compensation button to change the lightmeter setting (which is the only thing the exposure meter changes in Manual mode) to the exact middle so I can have an easy indicator that I need to adjust my settings by 1/3 or 1/2 stop or redo the whole dial-in process if there is a larger difference.
Anyway: Nice dogs!
DSC_0018.NEF.xmp (8.4 KB) darktable 3.5.0+2096~g629a0481d