From what I've seen they said they would try to have all the commanders balanced, so if you didn't have one, you will not at a huge disadvantage.
Check out the video's that HelpingHans did at London, they talk about commanders specifically in there among other things.
http://www.youtube.com/watch?feature=player_embedded&v=KLsHxprtOmc
I don't have 20 minutes to spend watching Relic say they're going to balance the game. Literally no RTS developer in the history of the world has ever straight up said "yeah, we're going to fuck a few things up and our game is going to be unbalanced." But look at Relic's history. Were all the doctrines in CoH balanced? Tell me that after the Pershing wasn't OP and Calliopes lost their main gun if anyone ever picked Armor Company except to rush a quick M8 or something. How many Wehr players went Defensive until the tree got buffed? Who the hell goes Royal Artillery? And Scorched Earth was a joke since the day OF came out. Not to mention other non-doctrine stuff that was just as unbalanced, like T-17 spam.
If I trusted Relic to be as good as Blizzard at balancing RTS games, then I'd trust them when they say that buying the collector's edition isn't going to give someone an advantage. Balancing RTS games is SUPER hard though, and Relic hasn't shown much aptitude for it in the past.