The fundamental difference is that CadQuery uses that jQuery-inspired fluent syntax, with a sort of metalanguage for some aspects, and Build123D is more pythonic with two different more procedural syntaxes.

The other big difference (which I have only read about) is in the way their assembly constraints work; again Build123D takes the more procedural approach (declaring "joints" etc.)

CadQuery came first; Build123D is sort of a more pythonic, robust restatement of it.