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FSQ and 11002 chip are an excellent combo and seem to work together beautifully.
The 50% QE is not that big of a deal. 80% QE is most likely a small chip and that has its own issues and may not match an FSQ very well which is after all a widefield imaging instrument so a large sensor is ideal and F5 is fast anyway so 50% is not problem.
QE is one of a string of factors to consider for what is best for a certain type of image. It may not that high a priority in widefield and quite high if you want to do long focal length narrowband (which you aren't intending per your post).
Greg.
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