I think you’re missing the point. As far as itemisation goes, Blizzard specifically seeks to make stats generic in the sense that everyone “uses” every stat, so that they can sprinkle in any of which stat at any point. If they feel like making a Crit trinket, they will do it because “All specs can use crit”. Mastery is in the same vein.
The fact that it ranks so poorly for certain specs on stat weighs is an issue, but not one they will ever address by “not putting in Mastery trinkets”. They won’t just do primary stats to get around the issue, because they LIKE the idea of varying up the stats. If it isn’t Mastery, it will be Crit that sucks next expansion, or Haste, and you’ll be exactly back in the same boat itemisation wise.
The only way to minimise the effect is to try and keep stat balance as close as possible, and since we don’t dev, the only option is feedback. They have occasionally backed off from truly terrible ideas, or given stats massive buffs to specs (e.g. Feral with haste). But at the same time, they don’t really pay attention to classes or specs when itemising - I distinctly remember ToC swimming in Defense gear for tanks, Ulduar had an overflow of Hit, ToC had an overflow of Expertise, etc.