Yup. Think of it as there being one markup on a complete bike versus a bunch of markups on individual parts. Even just in shipping costs, the bike in its box is one piece, while all the components arrive in other boxes and multiple shipping pieces, often not even on the same truck.

I saved money on my last build only because I got nearly everything on sale, used, or at a shop liquidation. It still wasn't cheap, mind you, but it was cheaper than it would have been for a complete new bike of identical parts.