"Markup" (and its relative "gross margin") are defined in terms of selling price versus the cost of sale.
For a producer, the selling price is the wholesale price, for a retailer, it is the retail price. Despite Apple's own retail presence, the vast majority of iPhone sales is through carrier and other retailers, not through Apple Stores.
The cost of sale includes not just the production cost (materials, labor) but also supply chain, unit tariffs and royalties, shipping in, etc.
Anyways, Apple's gross margin over all products has ranged between ~40% to ~47% percent since the rise of the iPhone. This works out to a markup of 66% to 88% across all sales. Now if we assume that iPhones are particularly profitable, with estimated margins of up to 55%, that works out to a markup of ~120%. While not bad, it isn't 200%.
And, it doesn't include R&D, administration, marketing, legal, rent, taxes, etc., which also go against profit.