Emacs' LilyPond-mode is an abomination in desperate need of maintenance
or possibly rewriting from scratch. There is no reason to use it unless
you are one of those people who use Emacs for everything (in contrast,
the mail/news client I am writing this in would be a reason to switch to
Emacs rather than vice versa. As are the LaTeX modes). However, it
probably has the only useable MIDI pitch recognition for polyphonic
entry like those of accordions.
If I needed to batch-convert some input regarding relative/absolute or
transpose, I'd likely start up Frescobaldi. Never mind that it isn't
the one editor to bring them all and in the darkness bind them.