SDL2 was not "just SDL1 with explicit window handles". There were a variety of changes and new features all over the API, including (like SDL3) major changes to the graphics subsystem (SDL1 used software rendering, SDL2 added hardware acceleration).

Also, SDL2 has evolved considerably since 2.0.0, and SDL3 continues that evolution while allowing API-breaking changes. SDL3 is not a from-scratch re-write and as an SDL user I dont anticipate migrating from SDL2 to SDL3 will be that difficult.

[edit] And SDL1/2 was never so "thin" that it didn't have its own high-level graphics system, which is useful to have out-of-the-box so that new/basic users can get stuff on screen right away.

[edit2] As ahefner points out, SDL1 was pretty "thin" by modern standards, but it still gave you enough to draw basic stuff on screen without writing your own pixel math, which was pretty helpful back in the 90's.