I agree about avoiding dealerships. Labor rates there are higher than at independent shops, which accounts for part of your bill.
$200 or so for a dealer-supplied alternator isn’t too bad. It was probably remanufactured (most replacement engine electrical components are nowadays) and even some dealer-supplied reman alternators can run up to and beyond $300.
Unfortunately, this may have been your best option. I know of independent shops which will not warranty their labor if they install aftermarket engine electrical parts. While these parts typically come with warranties of their own, some previously reliable remanufacturers have begun putting some pretty shoddy work out into the market. Cheap reman alternators and starters from AZ are notorious for failing within months of installation. (BTW, Bosch batteries from AZ are actually pretty good, if that’s the brand you bought.)
Also, it is true that the shop will need your old alt if they installed a reman. You can ask for it back, but expect to pay a “core charge” of around $50-$60. THat’s what they get charged for not returning the “core” to be remanufactured itself.
I’d say you might have paid $50 or so more than was really necessary, but as they say in the business: “It costs what it costs.” It’s worth as much as it means for you to have a working vehicle. Remember (at least from the independent mechanic POV), there’s rent to be paid, tools to be replaced, mechanics to pay, expensive ECU scanners (thousands in hardware and software) to buy, lifts to pay off, utility bills, haz. mat. disposal fees, extensive insurance fees, etc etc. You may think shops are raking in the dough, but many are barely treading water (not that this justifies ripping anyone off, but just to give you some perspective on why things cost what they do.)
But, yes, get an estimate first. Ask for one that states explicitly anything such as “Customer agrees that final total may exceed estimate by X%.” If they try to charge you more, in many states you have the right to demand your vehicle back. Failure to do so, as is my understanding, is considered “Theft by Withholding.” I know a mechanic that was arrested for such an offense, after a customer disputed work that was completed on his vehicle. You can bet that that mechanic got customers to sign a detailed repair authorization from that point on, so that there would be no dispute when time came to pay.
REmember: mechanics are like doctors. Find one BEFORE you’re sick and get a feel for his services.
I will step off my box now…