Your sense of "fairness" is showing.
Fairness--and I have no idea why you put that word in quotes, so I'm just gonna ignore that for now--is NOT what I was going for, so much as clarity.
If you have Mercurial Magic, and as a result you roll a D16 instead of a D20 for a specific spell. You cast that spell as a second action. instead of rolling D14 (like anyone else would) you roll a D16. Is that right? And by that I mean, "is this what the designers intended?" To me, this seems like a rules loophole, not something that is designed to function in that way. However, I did not spend the past year or so play testing this game, so I don't know--it reads like a loophole/typo/something that isn't clear.
Of course, it COULD be you roll a D14 for secondary spells NO MATTER WHAT--doesn't matter if you normally roll a D14, D16, D20, D24, or a D30 for this spell, you ALWAYS roll it as a D14 for your secondary attack. That has a certain amount of logic to it (more so than above, at least), but, in my opinion, doesn't gell with the spirit of the Mercurial Magic tables, based on my limited understanding of how these work at the table.
Does that make more sense? Sorry, I apparently wasn't very clear in my questions about it in my earlier post.