I’m using the Version 2.5.1 (1141). The new Axes Coordinates setup feels strange. My wide master and my narrow master have slightly different stem values because of optical adjustments (one is 100, while the other one is 94). It feels strange having to put the same value of 100 for the weight in the Axes Coordinates (Masters palette) when I know the stem is 94. Otherwise the instances are messed up. Did I get this right?
You can have wight values as you wish. Just for variable font, you need to align them.
But when they are not aligned, the masters are in disorder on the View>Show Master Compatibility.
If they are the same perceived weight (which I believe they are from what you explain), I would not say it is strange to give them both the same value, on the contrary. In this case, differing values just make it difficult to find the proper designspace coordinates for the instances.
Yes Rainer, thank you, that is exactly my point. You used the perfect word: perceived weight! I’m just saying it should be somehow better explained in the UI, because I get the same awkward feeling when I’m setting up instances later and have to put the same perceived value in the Info>Instances>Axes Coordinates>Weight. And the little info box only advises you to put the value of a representative stem width.
I understand how it works, I’m just saying it feels like a hack. 
The representative stem width is just a suggestion. Use whatever value you like.