I fear you have a point on the replacing int matter and the int stacking, though numbers are a little skewed. I just looked on my logs and I had 27.4% uptime on Darkglow buff on the sole fight I healed this lockout which is approximately equivalent to 822 spirit, but it could go to a theoretically maximum of 900 spirit.
http://www.worldoflogs.com/reports/x.../1/?s=73&e=609
Given that it is replacing a 180 int enchant and that they are roughly worth 2:1, on that fight it was a 462 spirit bonus, sometimes could go to a 540 spirit bonus.
That is *close* to alchemy perk, however alchemy perk for spirit means flasking spirit which is a big NO since you can gem on a 2:1 ratio. So based on the premise of stacking stats, alchemy perk for spirit (480 spirit over 320 int) is actually a loss.
I guess we can treat the matter just like hit caps for DPS specs, spirit takes priority over int until the 'raid is alive' threshold. There is indeed no beating BS for secondaries though.