OK. I suspect that the custom prefix ended up putting the gsettings schema someplace useless, leading to that error. I'll have to check the build scripts to try to figure out what is supposed to happen.
In the meantime, you could try running Geary from your build directory, and see if that gets around this problem.
PS: BTW, there was another error when I made 'make' which was due to the absence of gobject-introspection. It seems to me that this absence should have been detected by the ./configure script.
Could you report a bug about this?
Thanks,
Robert