I think it's odd that MrMalty doesn't have more functionality for a stepped starter, given that in White and Zainasheffs book they highlight the effects of inoculation rate on yeast growth. Sean Terrill has a process that's a workaround, but how hard would it be to set it up for stepped starters and different target pitching rates?
I've made an excel sheet based on their research in "Yeast" for my calculations. That's usually what I'll use when I'm trying to figure out my stepped starter sizes, but I still use mrmalty occasionally.