The main issue with calculating phylogenies or genetic distances including insertions and deletions, is that insertions and deletions come in many different types. A whole gene or other large chunk of DNA can be inserted or deleted in a singe event and should not be "measured" the same way as an large number of single-base substitutions. Insertions and deletions of transposable elements are more frequent than similar sized regions that are not known to be transposable. The smaller in/dels also come in many types, such as those that are flanked by inverted repeats making a hairpin in the DNA or RNA temple, variable numbers of tandem repeats, etc... But in many cases it is again more likely for an insertion or deletion of n bases to happen at one time, than for n number of single base events to have happened.