The reason that escort fighters’ attack value is increased by Jet Power is that Jet Power directly affects fighters’ attack value. That increase applies in both normal combat and SBRs. In contrast, Increased Factory Production increases an IC’s ability to mobilize units, not the IPC value of its territory. Since bombing damage is limited by the IPC value of the territory, it is unaffected by IFP.
The mobilization capacity and the damage cap being based on two different numbers creates a little shift in the balance between how many points of damage are directly applied to production and how many are applied to “infrastructure”, as the numbers are no longer 50/50. However, the total damage exposure is unchanged. This is attributed to the increase in efficiency of the factories.
Basically, the designers felt that giving an increase in the number of damage points that can be applied would in effect be penalizing the player for getting the tech. However, part of the reason that IFP’s effects are now limited to ICs in territories worth three IPCs or more is so that situations like the one you’re talking about, where ICs can’t be shut down by SBRs, don’t occur.