You would have to see the entire track plan to understand why. The lower level is cutout because we need to support the middle and upper levels and it's easier and gives more options of support using open grid. The sheets on east side of the layout is the main (guts) of the layout. Turntable and roundhouse with tons of tracks and a couple diesel service buildings. Some people go strictly cutout, some people go strictly table top, and some people (like we are doing) use a combination of the 2 styles to suit our needs.
Open grid benchwork also leaves many more options when it comes to doing scenery. Our layout has 3 different levels of track so the scenery transition between levels will be a lot easier this way. You're right though, the cutout method is a lot of work but required on our lower level. Otherwise we would NOT have any access to the bottom of the middle and top levels of track for wiring and installation of switch machines.