This is a common experience when people first encounter Darktable (DT) and free software RAW development. Here’s my own post about it, from almost exactly a year ago:
In my case, the RAW development was very far from the JPG one. It turned out there were all sorts of issues with the shots, partly due to LED lights giving out of gamut colors which confused even the in-body JPEG rendering…
One of the problems we’re facing, if I understand this correctly, is that camera manufacturers (Nikon, Canon, etc) collaborate with Adobe to have their JPG development process reproduced in Lightroom (LR) more faithfully. This means the RAW development LR users first see is often close to the out of the camera (OOC) JPEG, because proprietary development algorithms from the camera are reproduced in LR. I found this particularly striking when working on pictures from my Fujifilm X-T2 camera.
An entire play RAW thread discussed the finer details of how that bridge (and its environment) could be rendered:
In the end, I think the experience of free software RAW processing is that you are not trying to reproduce the JPG or LR development. I understand you are not aiming to do that, but the reality is that development is a personal, maybe even artistic process that will yield vastly different results depending on your objectives and (in my case, lack of) skill. 
The way I browse RAWs is through Darktable, and I made it explicitely use the JPG thumbnails. This makes sense to me because it’s how I saw the shots when I was taking them, it’s often the shot I want. It does mean that I sometimes have to go uphill to go back to that JPG, but it’s a small price to pay to not have Adobe and/or Microsoft crap on my computers. 
I hope that helps…