Sound's like you're spot on with the coolant. People put profit margins on products they sell. I get it it, they take the time to keep stock on hand and purchase the inventory. But that's an awesome markup. Insanely high..
The non stock pick fee I'd have less of an issue with. If they don't have something in stock and need to either order it online or run by somewhere in person. I get that.
I have no idea what he's meaning by a recovery fee. If there's no coolant in the compressor you can totally dispose of it yourself. Most scrap yards would actually pay you for an AC compressor. Depending on the hassle I'd do it myself to save $100.
But yeah, I'd definitely get a 2nd and 3rd opinion. I don't work for Angieslist..but FWIW I signed up 2 years when remodeling a house the ex and I purchased. There were a few projects I felt more comfortable hiring out for. It worked out really well for me. It was a great resource. Once or twice I even found a skilled trade guy from Craigslist and then cross referenced his company on Angieslist and found out they had GREAT reviews. It saved me a ton of money and worked great. Just a thought.