IIRC MSBuild was the brain child of Alex Kipman, father of Kinect and HoloLens. As legend tells it he lashed up a demo version over a weekend and pitched it successfully in the corridor shortly thereafter. The rest is history.

MSBuild is essentially a clone ant, and it's not a bad tool per se. For the devdiv engineering team it allowed them to get off the horrible pre-msbuild project files.

The messiness came with solution files (since VS uses solution files and project files). Unfortunately, they left the also awful solution files around. And this added an alternate way to specify dependencies between projects. VS solution files are awful to maintain - just a bag of guids that makes resolving conflicts very hard for humans and VS is poor at automatically resolving them (very noticeable when you get >3 developers on a project).

The solution to the messiness would be to use an MSBuild project file instead of a solution file. It'd have to conform to a schema VS understands, but it's not rocket science. However, fixing this would require the VS source code and MSFT to accept a patch.

Using Visual Studio, gui or command line, uses the MSBuild engine though the VS wrapping does some internal caching that occasionally makes it wrong (ah! There's a cryptic flag that fixes this).