There is the outFile argument which is mentioned by the question you referenced but, as you state, it will compile everything into one file. You could create a second tsconfig.json file (named tsconfig.subset.json or something) which uses the includes/excludes options to specify only the files you want but if any of the included files references any of the excluded files you will get an exception (e.g. the specific files must be self contained).
If you have a single file which you can use as an entry point that references only the subset of files you want bundled up you could use rollup or webpack.
Otherwise, if you just want to specify some specific collection of files that aren't really self contained I do not know any tools that do that.