I hate to throw a lot of anecdotal stuff into a thread that's designed to be more numbers-centric but retrospectively you can't really discount the way that spirit/mastery interacts with fight mechanics or damage patterns.
Looking at the last two bosses of the tier from a heroic 25m perspective I dropped a lot of spirit in favor of mastery for Lei Shen because there's just so little healing to be done for the majority of the fight and even in P3 because of the heavy movement having limited spirt still allows for plenty of regen between times I can cast so having a mastery heavy build makes sense in that it can help shield melee/tanks while I'm out of range because of P3 Thunderstrucks.
For Ra-den which is a tank and spank with almost no movement, unlimited opportunity to melee the boss for SoI mana procs but a prolonged heavy damage phase of the fight I anticipated a greater need for regen than Lei Shen and regemmed to what my current armory shows plus went back to spirit flask/food when I was using int for Lei Shen. I went in to the last phase at 90%+ mana and still ended up mana starved and wished I'd stacked more spirit. Not that the fight is particularly difficult but the healing requirement is pretty high and had we been lesser geared or with one fewer healer it would have gone badly because of a lack of foresight with exactly how much regen I needed to maintain the required output.
I feel like we're back to the beginning with spirit vs. mastery being only moderately quantifiable because the numbers don't really tell the whole story. Yes, mastery sims higher than spirit but you only see the benefit if you can cast the spells that stack the shield to begin with. Once that breaks down then spirit becomes much more highly valued.