You could ask FlightCase Warehouse to build to your exact specification of course. They do have that facility. Or, if you like to create on your own terms, then have a look at Thomann's Live Case Builder (or named something similar) where a graphical interface will allow you to see what the final design will look like with your choice of hardware. A bit more expensive but not the most expensive cases I have seen.
I found that actually I needed the 44cm depth because I mounted a 4 way power adaptor on the back of the board permanently so that I could leave LT plugged in as well as some USB power adaptors, rather than having to unplug those every gig. Also, with the added depth it meant that straight instrument cables were not hanging off the back of the board to get stood on. (My board lived inside the flight case all the time.) To lift the board out of my flight case, well, the FCW boards actually have a cutaway on one corner meaning that you can get your hand underneath to lift it out. However, I did leave about 2cm between the edge of my LT and the board perimeter to help with getting it in and out.
I also bought some of those really thick stick on foam/rubber feet usually for house furniture to put on the bottom of my board. It did lift the board up so LT was more level with the lip of the FCW case, but mainly to make it sit on the floor more evenly and not get too messed up underneath when playing on uneven surfaces.