I really do not understand how the Advent Refinery system works.
The short answer is the Advent refinery system works.. badly. The longer answer...
Unlike TEC and Vasari, the refinery oriented Advent trade ports are only affected by extractors in their system, not adjacent ones.
The advent can use their trade ports for trade or ore/crystal, but not both.
If you assume 1 ore/crystal = 5 credits, you should never use it till you've got it researched to 17%, then only on planets with 4 extractors. Once you research it to 25%, its worthwhile on planets with 3 extractors. This assumes 100% allegience at the planet. If your allegiance is lower... just don't use it! If your allegiance is higher, and you're at 25%, you can go with it economically at 2 extractor planets.
If you're below these thresholds, its better to use the trade port to generate credits rather than resources.
The TEC and Vasari refineries are much more efficient, since they pull in from adoining planet extractors. The breakeven is 3.33 extractors. Hence the viable strategy of just putting one refinery in each gravwell works with little thought, or you can micro your placement with great precision to nudge your return up a little.