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Today I did some experimenting and got to the bottom of the issues I was referring to above. Turned out to be the algorithm I was using in PixInsight to do the upscaling from 2x2 to match the 1x1 size.
If you're interested, if you use the BatchPreProcessing script, for the image registration section they use StarAlignment with the default algorithm of "auto" which is actually, I believe, is one of the Lanczos algorithms. Changed that to some others and tested, and the best result I found was Bicubic B-spline.
The above would also apply if you were using StarAlignment, not just the BPP script.
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