Hello,
The navigation Web parts were designed with the ability to filter out the documents based on settings under Properties > Navigation. If you are using a standard repeater you would have to either use the WHERE condition or a customize the control to also check the same property as the navigation Web parts.
It makes sense to use A/B testing when you are trying to optimize the structure of an entire page, in which case you would have completely separate documents in the content tree. Otherwise if you are optimizing multiple variants of one page,
MVT tests may be more appropriate.
That won't work because the repeater won't find the documents in those paths - isn't that the idea?
The templates will not inherit correctly - set them manually under Properties > template. You can configure inheritance levels.
Back links wont work, any macros based off paths would break - This would be an issue with your custom code, not a limitation of the cms.
Configuring A/B or MVT testing requires additional work in order to get accurate results, it is up to you which approach to take.
Best Regards,
Sandro