Thanks for the advices!
I finally got to test the W10 scaling on HD screen to see if that was the cause, it was at 125% (the recommended for this screen), but now I understand why there is black borders :
I made a test on another computer with W10 and the same size as mine (1366x768), but the game windows was smaller by 2 pixels and so the letterbox scaled it down, I think this is what also happen on the HD screen, the game should be fitting the windows but since the size is wrong by -2 pixels, it scales down and so creates the black borders, this isn't a problem of windows being larger but smaller;
For the moment I'll go with resizable windows until V0.48 release, hoping it will fix it