All you need is to decrypt everything else (easy), and then use this or something like it to get a decrypted eboot.
A vpk is literally just a renamed zipfile.
It's rather time consuming, especially on a weaker PC. You have to re-encode the entire video to burn in the subs, and you lose video quality in the process.
I'm saying that to turn a softsubbed mkv into a hardsubbed mp4 is obnoxious. MP4 is also not terribly well compressed, and h.264 is actually more space efficient.
And the point is not "Is it a good idea"
The point is "Can it be done"
I suppose the built in one is ok, but it requires a bunch of hassle for anime. FFMpeg is basically as little overhead as possible, so it should probably work.