They can (and do) have room if they're designed from the ground up for it. The engines for diesel electric trains are so large because they need to be sized to drive power for peak energy (usually accelerating and hills). If the energy can be stored, the engines for hybrid locomotives themselves can (and are) smaller.

So far you're only seeing hybrid locomotives for trains that stop/start a lot (shunting trains and passenger rail). The cutover for freight will likely take decades because A) locomotive lifetimes are measured in decades and B) longer range freight usually has less stop/start, making it's economical delta less.

I would imagine long range freight would be more likely to have long stretches of uphill grade which would mess with the minimum battery size