Ouch, that's a lot of yearly maintenance. Would you recommend changing the default value or trying to make it dynamic/contextual in some way? Or perhaps just trying to draw the user's attention to it better?
My first inclination would be to base maintenance cost off cost of rebuilding (optionally overridable) -- in effect, you end up with a much lower percent of total value where you're basically paying for an expensive lot, and a much higher percent of total value in depressed markets (e.g. where you can get 100-year-old 7-bedroom for ~= national median home value).
Just guessing here, would it make more sense to base yearly maintenance on $/sq ft instead of overall property value? Would better take in to account expensive but modest (lower maintenance cost) versus huge home (higher maintenance cost).
$/sqft glosses over local labor costs, level of finish, landscaping, etc., which is why you see people suggesting 1-2% of value per year, though you're right that it would be an improvement to separate out the value of labor/materials from the value of a the bare lot.
Just draw the user's attention to this and any derived/estimated values. It's impossible to model this correctly without very specific regional data.