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Hi David,
To my knowledge STL11000M has KAI11002 interline sensor. As you mentioned, peak QE is about 50%, while KAF6303 (full frame) has peak 68% QE. Difference is QE is somehow significant, but with FSQ your camera will be very sensitive anyway, even in narrowband. One thing to consider is the need for larger filters with KAI11002. I have no direct experience in using such setup, but from seeing images on the net, I can second what Greg said - it surely would make a wonderful wide field and fast system.
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