Lilypond was started because programs such as Finale, Sibelius, or Overture by default produce a score layout that is well below publication quality. While the majority of musicians might be surprised to hear this, genuinely professional engravers know of the problems and they modify the score to meet their high standards. The occasional element clashes produced by Lilypond are very minor compared to the engraving problems produced by Finale or Sibelius.

I came across a score by Meridian Publishing, Inc. that quite clearly used the default output. Fine for casual use, unacceptable for publication.

Contrary to what zimbop says almost every aspect of Lilypond's output can be modified. Granted, figuring out how is not always very straightforward. But doing things such as adjusting spacing and moving elements to avoid clashes is usually fairly simple.

The high-quality output of Lilypond is due to the fact that they haven't spent any time developing a GUI, but rather focused on researching excellent engraving practices and developing Lilypond to reproduce them automatically. As a composer who takes pride in my scores, I have switched to Lilypond and do not intend to go back.

Lilypond is probably not for the person who likes to print up scores on the computer with a minimum of fuss. But Lilypond is for the composer or musician who is willing to spend a little more time in order to produce a beautiful score. And it really only takes a little more time once you become accustom to Lilypond's input. But it does have a reasonable learning curve.