I wouldn't use crop mode. It's not really that useful, since it leaves you to solve problems like this by yourself. If you use one of the other fullscreen modes, everything gets scaled for you.
I disagree there. So far it was really useful.. until it won't lets me positionate stuff. lol This have to do with the layer viewport which are moving somehow. So yeah i probably have to figure out myself the positionning but i am pretty sure i will end up hardcoding the stuff since i can't do anything automatic.
Everything would get scaled up but at integer value since its a pixel art game.. so that leave the game with huge black bar. Not very interesting for the end user. Setting the WindowsSize at startup by events would solve a lots of theses problems cause i would simply choose the best option based on user desire.