When thinking about MPPT, don't forget something that was specifically mentioned in that white paper - the real gains come when the battery is nearly dead. However, in general it's recommended to not take a battery below 50% if you want long battery life.
So, how much actual benefit you'll see from MPPT depends on how low you drain your battery.
If you regularly take your battery down below 50%, then you'll get more benefit from MPPT, but if you size your system so that the battery only goes down 50% and then gets recharged the next day by the solar, you won't see much benefit on average.
EDIT: So, if you design a system to get maximum benefit from MPPT (regularly discharge below 50%), you not only have to account for the extra cost of the MPPT charge controller, but also for the extra cost in terms of shorter battery life.
If you're trying to recharge a battery that is already above 50% charged, then the difference between PWM and MPPT isn't much; You can expect maybe 10%-15% overall better harvest with MPPT, often less. On a big solar array, such as for a house, 10% is a big deal, on a < 100w system...not so much.
EDIT: On your pricing figures, you left out shipping, which can add up to a significant number.