I recently ordered a PCB with a cutout from JLCPCB. Mine didn't show up either in their Gerber viewer but the PCB I received was correct.
I also put a comment inside the cutout saying "CUTOUT", I think I read somewhere that it would be wise to do that just in case.
I did use kicad though, and I did the cutout using edge cut layers. I expect it should still work with Altium all the same.