First, for your cube example above, don’t forget JoinEdge’s companion command UnjoinEdge. So instead of exploding your cube and then successively re-joining edges, you can just unjoin certain edges, then unroll.
As far as the dialog, well, I agree and disagree at the same time. I understand that for the use you are making of it - where you want to join individual edges that you know are good and within tolerance without having to globally join stuff - having the dialog pop up is annoying.
On the other hand, when it does pop up under other circumstances, and the deviation is less than the file tolerance, that indicates to me that something is wrong and one needs to check why it didn’t join normally. It might be a bug, or there might be something wrong with one or more of the edges. Forcing them to join may not be the best thing to do. It can also make objects invalid - so having CheckNewObjects active is extremely important when using JoinEdge.
WAIT - I’m being stupid (again)…
@siemen - I have a simple solution to your problem - it didn’t even occur to me to check until after I posted - there is a -dash version of -JoinEdge that bypasses the dialog.
! _-JoinEdge _Pause _Yes
The above will join any two edges without any dialog coming up… Use at your own risk of course.