On a GEM, the flip is mandatory.
This is not universally true.
The only reason to do a flip is to prevent a collision. Some mounts need to flip because they will collide with themselves. My AVX, for example would crash the axis housings into each other. Other mounts, like my Astro-Physics mounts can rotate both axes 360 degrees without conflict.
So with the Astro-Physics mounts, there are two considerations: Will the scope and imaging package collide with anything? And what about cable wrap?
Cable wrap is not really a consideration because to track from the eastern horizon to the western horizon requires only 180 degrees. If you start with the counterweights straight down and let it track for 12 hours, it will end up with the counterweights pointed straight up. There is no reason to track further than that, unless you want to image the ground.
So that just leaves the possibility of the telescope and imaging package being clear for the entire 12 hours. This is up to the user to figure out. And if things are clear, an Astro-Physics mount will allow you to track for the full 12 hours without a flip. And you can start the session two ways. You can either start with the scope on top, as I mentioned above, or you can start with the scope upside down and let it track into being right side up.
All that said, meridian flips are no big deal. Just about every modern imaging package will take care of it. And to remove the mystery, here's what "take care of it" actually means:
A goto GEM will track at least up to the meridian, and possibly farther. When it gets as far as you want to go, you just need to do a goto to the current target. The mount will see that the object is past the meridian and approach the target from the other side (this is the flip). Your software just needs to know when to issue that goto.
In most cases, the goto can happen any time after the target object has transited. In some cases, the mount is able to use a reference other than the actual meridian to know when to approach from the other side. That scenario is a bit more complicated because the imaging software needs and mount need to agree on that reference.
It's not any more complicated than that.