If this was an education issue with kids from different schools or different teachers getting marked harder or softer, then the answer devised was moderation where the work of one student is compared to another and the results looked at. In my day we had, for example, ASAT exams that ranked schools and were used to modify your marks and achieve a TE Score that was used for Uni entrance.
Application here? I think a Conference system is a good idea for the game and the way Super Rugby is structured with SA, NZ and AU. I get why they have done it this way and the reasons are sound in a "greater good" way, which is how you need to look at it. But - the end result still needs to be fair.
So if you can't have every team play every other team twice (home and away) - which I think is the best option and haven't seen a really compelling argument against yet - then maybe the finals system needs tweaking and for there to be some "moderation" of results based on some sort of Conference Strength Score that is applied to the 3 teams that go through to the finals after the conference winners and which is used in relation to who gets the advantage of home finals games.
And lastly, how likely is it that a Conference winning side won't deserve a place in the final 6? It's got to be incredibly unlikely that a conference winner wont be in the top 6 surely, even this season the Reds made it, and on points the Brumbies would have if the Reds didn't pip them. And both teams had challenging seasons with injuries etc.
To me the issue can be confined to how the 3 other places are decided and who gets home finals. It's not that hard to tweak for a fairer result if you won't expand the number of games played.