I ran into this same problem. The issue is that the default config in the Yealink T46G has port 5061 assigned to TLS. So, when provisioning through EPM, TLS is not changed to another port. The T46G doesn't resolve this conflict and can never register. To fix it, you have 2 options:
In the Phone Config GUI, (the IP address of your phone), in the SIP settings, change the TLS port to anything other than 5060 or 5061. For example, you could use 5065.
In the Asterisk PJSIP settings in FreePBX, change the PJSIP port to something other than 5061 (if that is what it currently is). For example, try assigning port 5065 to PJSIP.
If you use option 2, rebuild the device configs, then reboot the phone to download the new config from EPM. Your phone should register fine after that. Frankly, option 2 is probably the better choice. Then, you won't have to log in to every phone to adjust the TLS port.