For what it's worth, I don't see the "cleanup".
If it significantly reduced the size of the largest directory,
that would be a win. But moving everything into src/ doesn't
do that.
If there's a way to divide the source into cohesive subunits, that
would be great. A programmer could ignore whole subdirectories
when working on something.
But just moving the whole existing pile into a subdirectory "because
everyone else does it" is not a reason; that's superstition.
Having to type "src/" a lot more often is definitely a downside.
Heck, that's one thing I actively dislike about GNU autoconf conventions.
If there's a compelling reason to change, could someone please describe it?