See if running this fixes the issue:
sudo /usr/local/tce.installed/gtk3
Yes, it does. I guess the gtk3 startup script normally waits until after all applications in onboot.lst are loaded? The script looks too simple for that. There must be something else going on.
OK, but each extension that adds gschemas needs to run glib-compile-schemas.
That sounds like a cleaner, more standard solution than bundling pre-compiled schemas.
I just submitted a cleaned-up gnumeric.tcz with all the above fixes. It works as expected whether loaded via onboot.lst or later.