I am also on Arch Linux with a recent GrapheneOS install on a Pixel 9 Pro XL. I have also tried both aft-mtp-mount and mtpfs and get the same results as you describe, as well as those in the linked github issue. I am just trying this since yesterday, so have not ever seen it working. Unfortunately I don't have any further info regarding what's wrong or how to resolve it.
GrapheneOS build number: 2025031400
android-file-transfer: 4.3
android-udev: 20250314
android-tools: 35.0.2
libmtp: 1.1.22