What's the trigger on Silent Fire? Is it just "the first 12 shots each day are silent?" Because I don't see why you're not making it unlimited-uses, like the self-spanning crossbow.
I agree, you're probably better off silencing the crossbow itself to avoid getting the bolt pink-dotted. Silencing the bolt will not protect it against Shriek of Impending Shafts because the only one who hears that is the magus who cast it. (Also? The way around that would be to use metal bolts.)
My own variant on the autoloading crossbow was here: https://forum.atlas-games.com/t/intellego-and-warping/142/1. I ruled that spanning an arbalest immediately was "very unnatural," though you went with "slightly." Also, since I made the crossbow magazine-fed and the bolt autoloading, I added a +1 complexity modifier to the enchantment.