One large + of the option to waive is that during months where you want extended amounts of off time together you are able to pile your working time together. For example if I want the first 12 days of a month off I can waive below 4, perhaps to even just 1 day off between work blocks, and request the desired dates. Depending on how you setup a bid like this PBS will attempt to put all of your pairings from the 13th to the end of the month. Imagine you already had vacation during that same month, you would have a good chance at having most of a month off. Then add in a bid in the month before that where you did the same thing but instead requested the last 10 days of the month off and waived the 4 day in order to get your trips at the beginning of that month; you would have the ability to have over a month off.
Obviously PBS will honor seniority in these requests and it might not be able to honor the entire length of off days you requested, but you can still do it. If the option to waive is taken away you are left with only the vacation time awarded and the availability in the red/green board. This is only one major benefit of being able to waive.