Canonically, they considered the Shivan tracking significant. Canonically, the Ancients figured out how to track capital ships in subspace thousands of years ago. Endgame suggested that the Shivans would be capable of reopening the Sol jump nodes, given enough time. I believe it was the FS2 tech room Shivan article that stated the Ancients claimed the Shivans were sensitive to subspace disturbances. And the various references to their use of uncharted/unstable nodes.
It may not be outright stated, but unless the Shivans were actually plotting a Xanatos Gambit involving the possible capture of the Taranis(putting beacons on it just in case?), I think it's a little unreasonable to assume the Shivans did not then have the subspace technology/expertise to track large ships just as the Ancients did 8000 years prior.
There are many things wrong here.
The first is that the GTA (at large?) at the time had no conception of how Shivan comms worked or ability to intercept them.
Endgame doesn't know what the ****. The guy's just talking to himself like a lunatic. There's absolutely no reason, anywhere else in the game, to assume the Shivans can do anything he says. ST and FS2 don't help the case either. EDIT: Or put another way, Endgame is about the same level of usefulness as Petrarch talking about what the Shivans were doing at Capella. It's an ingame character talking about something he has no possible way of knowing or understanding. The chances of Unreliable Narrator are very high.
The Techroom claims subspace disturbances, which could mean nearly anything. Given what the FS1 Techroom also claims about Shivan strategic priorities, it is far more likely that this means subspace nodes than anything else.
The Taranis is a combatant Shivan ship and you are seriously telling me that it won't have a functional comm system that could be used to send a distress call,
or an emergency beacon to indicate the ship is in distress. To quote Heinlein, any race capable of building spacecraft is not stupid. There were Shivan ships in the system it was taken to, explicitly, during the mission it's taken there. It would have taken them only minutes to get out a distress call to those ships and from there the Shivans could have shadowed it at long range back to Tombaugh.
While I generally agree with the proposition the Shivans have similar subspace tracking capabilities to the GTVA, there is no actual evidence for that proposition. It's all well and good to say it's so, but if you have to prove it, you're out of luck. And we can't prove it.