But I don't understand why throughput will be higher for longer pipelines, that doesn't make sense to me. I think that throughput in a segment should be based on the component in that segment with the lowest throughput. But if everything is simply pipes, then I think throughput should simply be ...

As described in FFF-364 for release 1.1 the intent is to disallow a blueprint from flipping if it would break.

The below image shows two inserter & belt builds (left) that break when flipped (right).
The first example is intended to put a different resource on each belt lane, but mixes them when ...