Yeah, so some of this comes down to "if we're in there, why not replace it". In my experience (and again, I'm a complete stranger on the internet) it's not necessary to replace everything. It does provide a level of assurance, though.
Sidebar:: Parts markup is normal. In my experience, I can purchase parts cheaper online than our suppliers charge the shop. Online retailers cut out some middle men (which happens to be parts stores in this case). And most times, the price the shop receives is considered "wholesale" and is applied without tax. They are willing to pay that price because of the perks they get (hassle free returns and no restocking fees, free delivery, same day delivery, and supplier back warranty and even labor coverage in some cases)
Dont get too hung up on parts prices. Labor rates cover tech's wages, L&I, trainings, certifications, insurance (insurance is a bear in the shop), equipment, etc. Parts markup helps cover bills and subscriptions, service info, office and service staff, etc. And that extra cost you pay gives you a great warranty (3 years in your case; better than industry average btw) as well as the judgement and experience they bring to the job.
The list looks good. I question the need for the radiator (as you said it was replaced a few years ago), vvt solenoids and the cam gears (phasers/actuators). Sure they technically wear, but I've never had to replace any due to wear (only lack of maintenance causing carbon buildup). And the solenoids are easy to replace as they fail. Unless you have noise or codes (or if you've really skimped on maintenance) theres little functional advantage to replacing them.
Maybe ask about those and see if you're happy with the explanation.
The machine shop work seems high, but good shops charge well for their work and without an itemized list of their services, I dont feel confident speaking on the charges.
Edit: it also looks like they have coolant on there twice (totaling 3 gallons)