It appears as if when two continents point at a single factory where one is Universal and another is AutoCapture, the factory territory is Captured.. It doesn't seem to matter what the values of the bonuses are ..or the order of execution.

I've posted an image and some comments on the wiki.. 

Yes this is by design - AutoCapture factories are dealt with after the rest of the factory actions take place.

This is done to prevent loop conditions.

But the values are summed, regardless of the function?

I still don't understand how it would be possible to loop factories when they only "fire" once.

A. The list is populated.

B. The list is executed (in some kind of order).

I can see where there might be contradiction that could be solved with hierarchical resolution, but if factories fire in order - and only once - how can there be a loop?