Peter, i have extensively modded a number of Canons, mostly 450Ds. yes you are correct with your assumptions. A camera which retains a Bayer matrix will not have the same capability as one which has had the matrix removed. Removing the Bayer matrix is a very difficult job, but it can be done, the usual most successful way is to rub it off by hand. In my experience, my success rate was one In three, meaning I would try three and get one that was useful. I used to buy replacement sensors from China and the USA. The technique is published online so I won't go over it here. But some tools would be required, a good circular magnifier light is essential in my opinion.
As to shooting Ha with the matrix still in place, yes, it will take a longer time, but do some trials on a heavy Ha target to get a reference.
Have fun.
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