Definitely an interesting question.
As long as you're not clipping digital signal at any point in the spectrum I'd argue that you should only use the modded-camera. It will contain the spectrum you'd obtain from the stock camera plus great red/Ha.
Almost any astrophotography needs colour balancing these days and you can control colour balance as you wish within software (as long as no data was clipped during collection phase).
You won't/shouldn't increase your signal to noise in any way combining stock and modded (over just using the modded for the longer total period) and certainly won't gain in resolution.
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