Offhand, I don't think you were ripped at all for the following reasons.
One is that WD-40 or Break Free is not a very good product for freeing up anything.
The other part of this comment is that rust is probably not an issue at all. The service manager was just blabbing this as part of the "Pacification Program".
Most service managers are mechanically clueless and often lack a backbone. It's easier for them to yak BS rather than be blunt and upfront about things.
Two is that you cannot compare one dealer to another and especially not to an independent shop. Each has their own set of expenses to cover and a dealer's expenses are far higher than an independent shop. That's comparing apples to oranges.
Three is the prices you did pay. The dealer, and independent shops, all mark parts up some. They HAVE to or they cease to exist. Here's an example.
The 279 is within reason and the 311 in labor can also be about right. Figure flat rate X the shop flat rate hourly charge and keep in mind that labor rates are far higher in many areas than others. The coasts are generally far higher than the country's mid-section.
Shop supply charge? Most shops charge this and some bury it in other places where it's not so noticeable. This covers the incidentals and supplies used in a shop, and believe me, there's a ton of them.
The only thing out of kilter IMHO is the "refurbished alternator", which I agree with oldschool is somewhat odd for a dealer to do. They will generally use a brand new factory alternator and of course, a new OEM alternator is pricy for almost any car.
If they did not have the alternator in stock and either you or they wanted to get the car done as soon as possible then I could see the reman alternator.
Just my opinion anyway.