By the way Alex, did this post inspire you to create the command channel perchance? It reads a bit like a lore-prelude to only being able to open a channel for a few seconds.
Yes and no. I did read that post a while ago, and remember it, so it conceivably played a role. The motivation/lore justification is different, though.
Initially, the command channel mechanic wasn't there - instead, orders were free under a set of circumstances (such as: assigning to a refundable assignment, assigning after a ship was already assigned to that assignment via a direct order and the game hadn't been unpaused, and a few other cases). That worked fine mechanics-wise but actually conveying what's going on to the player was going to be an uphill battle. Enter a global "hey, you just spent a command point - stuff is now free for a while" counter.
As far as the lore/in-fiction justification, I think of it as calling a command conference among the captains. (Yeah, it's only a few game seconds, but combat time isn't the same as actual time.) There's only so many of these you can call before it becomes a fatal distraction, with better admirals being able to get more done.
I also had this crazy thought that you'd be pretty stupid to not pause with the channel open, how do you circumvent that?
Well, you're supposed/expected to pause when the channel is open - nothing to circumvent
The timer is just there so you have a little more flexibility - accidentally hitting the spacebar won't waste the command point, and if you only have a few orders to give, you don't have to break the flow by pausing.