From my understanding, the main purpose of energy is to limit the amount of "things" you can build at any given time. Additionally, it makes it easier for the AI to kill the player if the player lacks the energy buffer to maintain their defenses, hence the role of Matter Converters.
In the case of fleet ships, the caps provide a secondary limitation --- in the limit, to prevent the player from building a metric ton of ships for homeworld assaults. Furthermore, caps on auto-build-able ships prevent accidental energy exhaustion by telling the Dock when to stop.
However, I was looking at the modular fortress with its ship cap of 1 (and at fortresses in general) and got to wondering: given their high energy cost (ModForts at 100k, Forts at 90k, 120k, and 180k resp.) and the fact that they are must be manually placed rather than auto-built, what is the balancing purpose of having a galaxy-wide cap on their usage? By building them, I've already said that the system's defense is worth most of the free energy I gain from it (more than that in the case of FortIII), so why does the cap limit exist? What cheese is it preventing?
The main thing that I can see is the player putting a Fort on every border world, but at that point, shouldn't the energy costs --- in principle, I haven't crunched numbers --- cause a handicap on the amount of other things I can build, especially the ships I need to take the next planet / the AI Homeworlds?