I was never really big on buying magic items in games really. If you arbitrarily set an hourly wage to an alchemist, it's easy enough to calculate a materials+labor cost for it, but the twin factors of scarcity and danger make it tough to establish an actual price mark. . . .
If a +5 Broadsword is the best magic item the party has up to 10th level, then, it's actually priceless. (Or at least, irreplacable.). . .If you can buy 10 at Ye Magic Smithy and get one free. . . .well then perhaps it's worth 5% more than a normal sword. (Well, it does magic crits vs L and SL, so call it 10% more than a normal sword.) Most games fit somewhere between those extremes. . .but exactly where?
On the slip side, the risk of Spell Failure combustion is pretty high for an alchemist. . .they pay people who work with explosives an awful lot due to the inherant danger of the work. . .what's the markup for that?
The issue of pricing and scarcity for non magical bonus items is addressed in CT, at least there you can extrapolate a normal curve of more experienced craftsmen, then curve the pricing accordingly, no effort was made to replicate the rules in the Alchemy Companion in CT.
