Off the top of my head, in no particular order:

As the sibling comment mentioned, the classic problem of chamfer/fillet. Inconvenient in OpenSCAD, trivial in build123d.

There are various features I've missed: polylines with rounded corners, extruding along a path, and more I can't recall.

As you mention: code organization. I didn't have the need early on, but over time I often wanted to do add custom things, for example my own hack of an implementation for extruding along a path. And passing data around is just painful and ugly... since you can't read any of your input shapes, you have to pass around all data explicitly -- alongside or instead of shapes -- and then only actually render them in the latest stage. Generally I found it hard to make reusable code, and generally it has to make many assumptions about the calling code.

The OpenSCAD editor is one big IDE, and it's not a great one. My workflow was to keep VSCodium on one side and OpenSCAD on the other, just to use a better editor. I actually thought to myself that a good project direction would be to make it more modular and focus on the unique parts rather than the IDE. And that's indeed how build123d does it: primary repo only handles the rendering, and then suggest compatible viewers, with one shipped as a VS Code extension being the primary suggestion.

Speaking of workflow, a huge difference is local coordinate systems: lacked in OpenSCAD and encouraged in build123d. It fits my brain really well. I just made a shape, now I want to make some holes in it. Previously I've often had to think about what global coordinates to put some volume, but now I'll just select that face and work with those local 2D coordinates.

And another workflow annoyance before is when I'm designing something to be printed in separate parts. First, meticulously fit things together in the global coordinate system so that I can see them in the assembled state. Then to allow printing, also conditionally move all parts to manually specified other coordinates. With build123d one can define the parts separately, place joints in desired locations, and have them automatically snap together for the assembled view. It looks useful for integrating third-party parts as well.

Minor thing, but I'm always slightly annoyed by the fact that a rectangle is called a square and a slab/box called a cube in OpenSCAD...

Oh, and it's often useful to use polar coordinates. More passing around custom data and manually calling your custom conversion function whenever passing to OpenSCAD. build123d has first-party suitable objects for it.

OpenSCAD development seems fairly dormant as well. Latest stable release was five (!) years ago, but by reading around you see that you're supposed to use the nightly version because it's superior. Not very friendly for newcomers. By contrast, build123d seems very active.

I should stop now, because this already got pretty long. As you can see, I had some bottled up though -- thanks for letting me vent!

Build123d: A Python CAD programming library