I usually set up the hostname in vtysh.conf and it overrides the hostnames in frr.conf.

The interesting thing is it did seem to read my zebra.conf, but completely skipped the bgpd.conf.  So I tried copying the contents of the bgpd.conf into frr.conf and the daemon starts, and doing a show run it looks pretty identical to quagga system side by side with a few caveates (hostname for instance shows up twice with 2 different values).