Not only that, but I am CERTAIN I read somewhere that initially,
had wanted to make a single subspace vortex per group of emerging craft, such as an entire wing spawning from a single spot, but changed their minds (maybe for performance reasons?)
That's in the Reference Bible, for the FS1 intro. Something like, "Several portals opened, and from them, streams of Shivan fighters poured".
Well, aside from it never happening that way in any canon mission, the FS1 endgame cutscene does make it look possible. I got stuck earlier trying to make up something to describe what it's like to exit subspace. I mean, we got that one look at the Lucifer and the strike team exiting subspace, but it was from the outside, and there was no glimpse of what it looked like as the fighters
approached the destination.
The bit about the synchronization I basically said because it looks like the ships are moving rapidly through subspace (in in-subspace missions), even if their speed is zero. I figured, if that's what it looks like going one way, for ships going the other direction, I figured they shouldn't ever meet... I mean, the backgrounds for each would be going opposite directions, and anyway the ships are going faster than light in opposite directions (at least on the real-space side). Also, that was part of what I came up with to work in the need for sub 'tracking' technology.
I think that if you've "synchronized" your ship with the subspace (n-dimensional) frequency of another ship which is about to enter subspace (or is still en transit), you can follow it into its own subspace portal
Well, that's basically what I was trying to say, except I didn't feel like resorting to technobabble. Basically, you've got to match some not-incredibly-obvious and nigh-impossible-to-match-accidentally values the first ship used to enter subspace.
Another of the things I was basing some of this stuff on was the fact that it is possible for command to communicate with you during several missions when there are no allied space stations or warships or whatever in the area. That signaled to me that they'd have to be somehow sending messages through subspace. Also, you can obviously receive messages in subspace (as evident from Command panicking at you over the comm system as you try to stop the Lucifer). To me, it seemed odd that if there were so many different possible routes through a jump node such communication, that these messages could have been simultaneously entering
every conceivable path in order to communicate (that is, before the 'tracking' technology came along). So I figured they needed to use the same tracking info for that as for the pursuit-jump. As for communicating with the system on the other side (which I seem to recall was done at least once in one of the games), that might be easier to do, because regardless of which route through subspace the signal goes through, it would still end up in the correct system, and (depending on how the final heading is determined), possibly directed the right way. Of course, they might be using something else for that... maybe even quantum entanglement

... Actually, the fact that the sending of information faster than light using quantum entanglement is effectively sci-fi crap doesn't mean the phenomenon isn't useful for encrypted light-speed communication, and, in a FreeSpace context, possibly into and out of the fictional realm of subspace. But I'm just making stuff up, there.
It seems to me that, because there are so many more options as far as destination, and other stuff, with intra-system jumps it would be very difficult to utilize the sort of tracking that they used to take down the Luci... that, even if the ship could be tracked to its destination, by the time you could get in with it, it would already be at its destination. Also, now that I think about it, it seems like Command probably used the tracking tech to figure figure out that the Belisarius was heading for your convoy in "Surrender, Belisarius!"... but, since such tracking isn't widely available even by the time of FS2 (I seem to recall there being
Maybe the 'tracking' isn't necessary if the ships are friendly and transmit their jump information to each other... that would make that simpler anyway. I hadn't thought of that possibility, however, so I based that bit about it being impossible for ships making intra-system jumps to get messages from command on that...
As for what I said about Derelict, anyone saying it doesn't conflict has obviously forgotten that the Nyarlathotep was encountered drifting in subspace, and that the entire sequence featured ships (and debris) idling in the same subspace corridor for an extended period of time--ages, probably, for the debris.