Art Pipeline for textures, keeping your source files good or a bad pipeline? Thoughts about it?

I’m about 6 months into Unreal, and I find it really easy to clean up and structure working files folders.
In a conventional game pipeline,
The source folder mimics the folder that goes into the game, reason for it is to maintain the highest resolution and have the game folder be optimized for the engine.

But Unreal pipeline at times feels counter intuitive to keeping the source folder. Textures examples, .psds, that eventually becomes .pngs or tgas to eventually many .ua files that require prefixes to know what type of file they are.

Once a source file goes into unreal it can be radically modified, inside unreal, like manipulating your .ua textures inside Unreal or even telling at what size should they be, after all that iteration, It feels like an extra leg of the pipeline is always allocating time to mimic your game stuff.

Any thoughts on this? Different pipeline structures, or different thoughts on the way Unreal wants you to work?