Here's a fairly simple justification: the size of your shipyards. Tug+Terraformer is easier to build than Terraformer with engines.
I haven't actually used tugs, but here's how I think they'd be used:
You have a ship with just a crapton of engines and fuel. It doesn't need to have a tractor beam.
You have your terraformers, your jump gate builders, etc., possibly even fuel harvesters, each have one tractor beam, and one single max size and efficiency engine(just for emergencies and catching up with planets if something gets screwed up), in addition to whatever they're job is.
Tractor beam the things to be hauled to the tug, send the tug on it's way. All those terraformers will be hauled with it, for example. And the tugs can be used as shuttles too, taking important personnel or teams around your bases. Can haul PDCs if you stick a tractor beam on either end(or, have a link-ship; tiny ship with two tractor beams to allow your tugs to tow things without tractors beams on them).
But really, the biggest consideration is expense and shipyard size. A carrier to bring damaged ships back home that can move at the same speed the tug would is going to be really big, and really expensive.