The simplest way to solve it is to assume that every ship generates its own, very small, "pocket universe" to dump the heat into. However, if that is the case, then the problem of overloaded "black globe" capacitors would no longer be a problem. Also, if you can put energy into a "pocket universe", you should be able to draw energy back out of it, which would also mean that your power duration, assuming no maneuvering or jumping, could be extended enormously.
The other option is to assume that power requirements are severely overstated in the rules, and reduce them accordingly. However, that has a massive effect on your ship design sequence, so not the easiest option to put it.
A ship can have thermoelectric generators (that's what powers Curiousity), why waste the heat?