I searched around and the only reason I could see that people inline source maps is for use in development. Inlined source maps should not be used in production.
The rational for inlining the source maps with your minified files is that the browser is parsing the exact same JavaScript in development and production. Some minifiers like Closure Compiler do more than ‘just’ minify the code. Using the advanced options it can also do things like: dead code removal, function inlining, or aggressive variable renaming. This makes the minified code (potentially) functionally different than the source file.
This could still be done by referencing external source map files of course, but some people seem to prefer inlining for their build process.