I had a similar situation except I recently converted from CHAN_SIP to CHAN_PJSIP. Since the WebRTC ie 99### extensions were all setup from when it was CHAN_SIP the solution to my problem was different.
I used the GUI and Edited the User Ext in the Advanced Config I changed he option Enable WebRTC defaults to YES and this removed the 99### extension from the pjsip.endpont.conf so only the ### extention was listed and the WEBRTC client started working.
I think this was related to my converted from SIP to PJSIP and then I used the console utility to update all the clients to PJSIP. converting sip to pjsip wiki post I am going to make a recommendation that the tool also set the Enable WebRTC defaults to YES as part of the config change.
Having the 2nd Ext is only necessary when using CHAN_SIP because it can’t have more then one device registered to the same extension like CHAN_PJSIP can.