When you consider that all an enlarger timer is is a method of interrupting the flow of electricity to the light source for a specific and repeatable time, then it theoretically makes no difference whether it's on the 12v (lamp) of 240v (mains) side.

Using it on the mains side has some safety aspects to it as well as putting additional strain on the transformer. I don't think transformers like the constant surges of switching off and on, hence that's why the timer will have been on the output side of the transformer between it and the lamp.