@ alex_brunius:
In response to your points...
Cost: If we replace a 10000t fighter strike group with a 10000t warship of the same speed, total engine cost won't increase. Going bigger would allow installing all sorts of fluff, but as a direct replacement for the fighters it could be just as lean.
Research Cost: Size 400 may well be excessive, and that's quite an advanced tech anyway. But cutting down fuel use of the current generation by 2/3 (for which size-40 would be sufficient compared to fighter-sized engines) may be worth the expenditure. Fighters may also be forced to use excessively compact engines (requiring higher multiplier tech) to remain within 500t where warships can freely trade a little tonnage efficiency for considerably better fuel efficiency.
Explosion chance: Agreed somewhat, and there are other matters of redundancy - where a larger ship makes better use of passive defences, tiny ships make the opponent waste firepower on overkill.
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On to your question: Mostly the scaling of sensor footprint and fuel use. A very simplified take on it:
The reduction of sensor footprint by using fighters for missile delivery is very beneficial. If speed is no major objective, the losses in fuel efficiency won't be too relevant, and giving them a decent mission life is more economical than putting them in an expensive, highly visible and vulnerable carrier.
For fast, high-powered beam attackers, fuel consumption is a concern even if they spend most of their time in a hangar. On stressed ships, weight is the enemy; carting around more fuel means we need even more high-powered engines to maintain speed. Also, if I'm willing to spend the resources on speed, I may also want long beam range to take little or no return fire. Speed + long-ranged weapon + associated FC usually doesn't fit into 500t.
Sensor footprint isn't a major option if we need to cross the AMM envelope.