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DSS will warn you if your subs are of different lengths but not sure how it affects processing. Why not just use 'layering' in Photoshop to place the Trapezium short subs into longer gas cloud subs - is this not the standard way to process M42 - even though I have not done that myself -yet. I have a library of different length subs of M42 and you certainly need a short sub to grab the Trap stars without burn through. To get it perfect I think you would need multiple 'layers' as you work outward to the cloud detail. So it becomes a true processing creation as opposed to something you just shoot and stack. Back in my film printing past it was really easy to 'hold back' an area from over-exposure during printing by just waving a small paddle in the light stream from the print head to reduce light falling on the print paper. Something of an art but gave great results with over exposed negatives. Likewise you could burn in areas of under-exposure.
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