They certainly stack.
Howlrunner:
While another friendly squadron with Swarm at distance 1 is attacking another squadron, it may add 1 blue die to its attack pool.
Flight Controllers:
The anti-squadron armament of each squadron that you activate is increased by 1 blue die until the end of its activation.
NB, Howlrunner affects the Counter ability; Flight Controllers does not.
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Vertrucio wrote:So spending that much on these abilities only pays off if you're facing a lot of enemy squadrons, and you can get the drop on them with activations.
It's not just a matter of facing lots of squadrons -- it is also a matter of Rebel sqaudrons being stronger. Only Y-Wings are incapable of one-shotting TIE and TIE Interceptor squadrons. They need to benefit from both of these upgrades to do the same against Rebel squadrons (again, accept Y-Wings). But -- for that very reason -- you're certainly right about needing to get the jump on Rebels. After all, no matter if they're rolling three or five blue dice against squadrons, they still only have three hull points. This is where Howlrunner is particularly vulnerable.
Howlrunner also costs as much as two standard TIE squadron. Taking a standard TIE and Flight Controllers is still 2 points less than Howlrunner. I don't think that makes Howlrunner a worse choice, however, because her ability doesn't rely on a ship taking a certain command. This is especially important because of the screening role TIE squadrons often play. She remains
IMO the most important ace the Empire offers.