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I don't know about compensating for flexure between 2 mounted scopes but T-point does a good job of measuring and compensating for go-tos of non orthogonal aspects of your mount and also for various flexes.
If your 2 mounted scopes are flexing differently to one another that is a physical problem and as far as I know not solvable with software.
You would need a more rigid double mount. I think these setups tend to be problematic.
Greg.
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