Seriously, you get more time for passing checkpoints with EV's and more time for delivering the EMP charges on Chapel and I think you also get more time for delivering Virus samples on Bridge.
So why is Trainyard the odd one out? All it serves to do is make certain Trainyard situations unwinnable for the attacking team. It's pretty easy to deny the Datacore with Stoker or Kira and IIRC it only goes into overtime if your in the middle of delivering it (I may not be remembering correctly though).
It doesn't help that just getting the damn Data Cores to the thing is hard as @$!# because most of the paths you have to take to get them there are narrow, long hallways with no cover (one of which gives Defenders a height advantage