Come on...someone hit your car...you can't blame Lexus for that. I agree, only way to repair that and have it be 100% is to replace the hood, I would take it to a good shop and just do that. OEM windshields for ANY car cost $1,000+ if you pay out of pocket.
The protection package is for paintless dent removal, thats a bad dent and it isn't repairable with PDR. You can't expect them to fix every body damage for $1,000 upfront. Thats possibly a $1,000 repair right there. Lexus bulk autobody parts aren't expensive, bodywork just isn't cheap. Take it to a good independent body shop with references and get some estimates.
Just because its a *Lexus* doesn't make it immune to rocks hitting it or people running into it.
As for the $350 oil change, thats a 5k service including a tire rotation etc. On par with other luxury car dealers. Loaner cars, marble, cookies & coffee, flat screen TVs & jazz music don't come cheap. I recommend finding a good independent shop.