We used to be able to tune the spacing globally with \paper
parameters arithmetic_basicspace and arithmetic_multiplier, but they
are no longer in the reference manual, so they may have been removed.
Lily is particularly variable in her note spacing right now, but
global note spacing is an important element of style, so give them a
try :)
The space between notes is arithmetic_multiplier
arithmetic_multiplier * ( c + log2 (time) ) where time is the amount
of time a note occupies. The value of c is chosen such that the
smallest space within a measure is arithmetic_basicspace. The
smallest space is the one following the shortest note in the measure.
Typically arithmetic_basicspace is set to the width of a quarter note
head.
John