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I share your pain but that's what .NET standard requires. It states that MVID (UUID) can be used to distinguish between two versions of a module. That means same source code will produce different assembly.
Yes, that's what people end up doing. I'd just monodis the assembly then remove/replace MVID and do binary compare on that. It may not be exactly what you need performance wise but that's the simplest way I can think of.