Simply because {la djan kau} is arguably never correct, {kau} can never "replace" {ba'e}. {kau} has a particular use, namely to mark indirect *questions*. {kau} on anything but a question is weird, at best, and complete nonsense, at worst.
{ba'e} on the other hand marks emphasis. Emphasis and indirect questions are two separate ideas.
{.i mi djuno lo du'u xukau la djan ba'e broda} "I know whether John brodas (and not whether he does/is some other selbri)"
{.i mi djuno lo du'u ba'e xu kau la djan ba'e broda} "I know *whether* John brodas (and not if it pertains to some other indirect question)"
The thing about {makau} is that it's somewhat referentless, like {da}, and it's best to think about {[question]-kau} constructs as being single items of the [question]'s selma'o.
As for "replacing kau with ba'e", I must say that replacing *incorrect* usage of {kau}, such as {la djan kau}, with {ba'e}, in the form of {ba'e la djan} is a very excellent solution.