100 watts is a 100 watts so the heat should be the same but I still wouldn't do this for 3 reasons:

1. It is unlikely that the two lamps will be physically compatible so you may have to make mods to lamphouse/lampholder - see #3
2. I don't think a 240V/100W halogen lamp will have been designed for enlarger use and may fail early due to frequent switching. In colour printing you don't want to change lamps any more frequently than necessary
3. It is potentially dangerous! 240V is lethal and you will be introducing that potential into a device designed for 12v, possibly only lightly insulated and probably not earthed (although all enlargers should be)

In theory, the safest way to do what you propose would be to use the 240v output from the timer to drive the 12v100W transformer but I doubt that the timer output could handle the 8-9 amp current draw of the 12v lamp. Might be wisest to buy another timer and keep the 12v100w lamp. OzJohn