The problem with mp3 files and ogg files is the padding that is added at the start of each file, which makes it harder to find the perfect looping point as depending on the program it varies the silence delay at the start of a song.
That's the main reason behind the Loop Tuner patch I made for the game. The only real way to get a perfect loop is to go in-game and test the looping points in-engine, or have them cut like you mentioned.