I'm sure it has been stated that Free Companies would have their own chat channel and all that goodness, however I can't be bothered tracking down a quote. You will be tied to only one Free Company however, while still being able to be a part of any Linkshell community you wish for chatting.
Honestly, I think this will work well - has been a similiar system in a few other games and it helps you to keep up with friends who may not progress at the same speed as you (faster or slower) or just happen to move onto other things (a falling out within a guild, but not with the specific group they are close too within that guild) or just keep your social life and progression life seperate haha
Vanguard had a couple really funky chat channels outside this (that I wouldn't expect in this game haha) but had a certain class that used telepathy, and all of them could talk to each other in that specific channel!