The term "deductible" is usually associated with warranty or insurance claims. The warranty on a replacement OEM component is usually 1 year/X miles, depending on the component, and is always free. So it stands to reason that the $500 they're asking for probably isn't a deductible or a warranty cost. What would make the most sense is that Mazda is covering everything except for $500, which you're expected to pay out of pocket, or Mazda is covering everything and the dealership is trying to charge you $500 to recoup costs and/or make this repair profitable for them, as you mentioned previously. If you want, you could ask for an itemized invoice, telling them that you will follow up with Mazda Corporate to confirm the associated costs, warranty, and parts are correct. Just say you're doing your due diligence.
All told, $500 isn't bad at all for what you're getting. The cylinder head crack is a known and well-documented issue, so it wouldn't be as hard to get the head replaced out of warranty if you needed to, but there are no guarantees since it is out of warranty regardless. I guess what I'm saying is that if it were me, I'd push to find out where that $500 is coming from to see if it's something you should be charged, but if it came down to it, I'd pay the $500. To me, it's not a hill worth dying on.