Yes, Render In Place is one alternative, but it would be nice to be able to use the Freeze capability even when using the Arranger Track. The solution I found was instead of trying to flatten an arrangement, to just activate that particular arranger chain, and then just do an audio export of that arrangement. While that still doesn’t give you a freestanding new Cubase project with the new arrangement, if you’re just trying to do different “cuts” of the same song, that might work for you.
When doing that, I ran into another issue that seems to be a bug, and I’ve tagged it as such in a different post:
https://forums.steinberg.net/t/export-length-issue-with-arranger-track-active/731301