You can work around that, but let's be real, that's just an embarassing bug.
What should happen:
- selected loadout applies reinforcement slot configuration of capital ship
- selected loadout applies preconfigured ships
What really happens:
- selected loadout applies preconfigured ships within open slots
- capital ship change applies RF slot configuration change
- open slots are automatically filled (based on ship power)
Something like that SHOULD have been prevented in the design phase of the new fleets feature, as it is glaringly obvious.
At the very least, this should have been fixed on any tests of the feature before release. Again because it's so obvious.