Since the FDL likely operates at >100% Power in full gear - it has the same problems as all other Ships have :
If you stuff it with power-hungry equipment that tops-off its Power Plant capabilities, your Fuel Scooping performance will be degraded due to the lower Temperature Delta the Engine can still safely cool away.
Solution for any Ship :
- place yourself above, aiming onto or below the Sun at 30km/sec
- try disabling all Weapons, even Shield or Shield Boosters doing the exact same and compare temperatures & scooping rate available at 65% heat
You'll see it makes a rather drastic difference.
If you're used to "performance scopping" (circle the Sun at higher speeds to increase scooping rate), you're naturally more prone to overheat your ship (although it can be done if you find the "sweet spot" and are able to maintain that).