I have this problem on one Android device. I suspect that something may be wrong with the ROM (which is an unofficial release of LineageOS), but still. Basically, despite that fact that Syncthing is running as root, it cannot access some files with permission errors as follows.
Yeah, I suspect some misconfiguration in the ROM, as I have encountered some other problems, e.g. when trying to download a file using the Web browser, etc.
However, if I use adb shell with su, then I can access/modify/delete the files, so the behaviour is not consistent. I am going to downgrade to the last official version of LineageOS and see whether the issue stands there too.
FWIW, one of the reasons my computers use FUSE encfs systems is because root cannot read the plaintext mount; it can read the encrypted volume, good for backup and restore, but meaningless gibberish until mounted properly.
I don’t know enough about Android to know if this matters.