Is it because the first two were prototypes so they bolted on whatever they needed without care for it looking nice or did they just refine it so much that they were able to simplify the design significantly?
That and the march of progress, despite what some people believe we are still evolving at a rapid pace and engine outputs have significantly increased recently.
It's more of a refinement thing, where anything not absolutely necessary is removed, or 3D printed straight into the structure of the thing instead of added to the side.
FWIW the Raptor 3 here does not include the turbopump mechanism. It would look pretty much the same as the raptor 2 (which does have the pump attached).