I think that the rootDir field of the tsconfig.json is currently not used by tsify.
A problem only exists when you use an es5 or es6 entry file for browserify and have no ts file in the same directory. The ts fiels will be recognized by tsify but are not cahced with the right folder structure so that they are not found by getCompiledFile.

The workaround is creating an empty ts file in the directory of the browserify entry file.