What you're missing is that these big engines are also game development environments with extensive tools and integrated market places to purchase assets and features.
Learning Unity is learning an entire platform. It's a marketable skill.
Generally smaller developers don't have the development resources to roll custom everything. But modern platforms have enough spare hardware resources that the inefficiencies of Unity are worthwhile.
An engine like unity basically provides utilities such as physically based rendering, camera systems, visual editors, scripting environments, a scenegraph editor, preview windows, io, asset import and conversion, audio, etc. Some games are of course easier to make than others in such engines, but they aren't that prescriptive.