You will want to plenum the intake or exhaust from up high, or add a fan to keep the air stirred up, but down low is common on ultralite rigs--popups, teardrops, etc.
I think it is a fair trade for the lower COG and roof height. No way would I put a roof air on a 4wd, just asking for trouble.
You can get super-efficient window units these days that run from the little Honda genny just fine.
Make sure you understand how the outside fan cycles air (usually pulls from a side and pushes out the front or vice-versa) and set up your vents and spacing accordingly. If you don't, the box will heat up to the point you won't be making cool air. Some end up adding booster fans to vent the box if they screw up, or mounting the unit on a slider so it pushes out in use.