Here the solution to all my problems (desktop platform).. i just programmed this in C# for my game. The settings are wrote to a single .txt file that the game is loading after.. plus it handle system screen resolution change and set it back when the game end.
I use crop mode, screen size is small.. and when i get to fullscreen or any window size.. everything is repositionned with Viewport properties. All layouts are scrolled to 0,0 automatically (except the ingame layout) which make the layout at top,left position and resizing is done to the right, bottom.
End. :) and it work flawless.. if he desire fullscreen he can.. if he doesn't he can too! plus an extra where he can choose the scenario to load. But the point is that there are many option for a desktop user.. sure this kind of thing won't work on mobile.. but then you can adapt so it use integer scale and forget about the rest.
And guess what ?.. no seams at all.. whatever the resolution is used. How this is possible ? simple.. there no scaling at the game. Only screen resolution got changed and this is the technique used by many desktop games.