I mean, if you open the waste tank, you see that there is only absorbing material, the chip is connected to nothing. The chip is maybe just an ID number. It has no way to see the psysical hack of the absorber.
Like the chip in each of the ink tanks... the chip in the maintenance tank is merely a counter that is written-to to mark the state of its consumption. There is no sensing mechanism.
With the iPF6100, the maintenance tank chip's counter can be reset back to 100% in the service menu only if the counter does not drop below 20%. Past (lower than) 20%, you're SOL.
The point of the shaped absorbent media in the maintenance tank is probably so that the tank doesn't foam over (and presumably into the printer, where it could do harm). Suction of ink mixed with air is sure to produce bubbles, if not outright foam. Foam is quickly dissipated by contact with highly-breathable media that breaks the surface tension of the bubbles.
Whereas I think the difference is probably limited between the engineered absorbent media and just wads of paper towels, I'm of the idea that short of Mfg-recommended replacement of the tank... the next best thing is probably to simply rinse out the media. They clean-up much better than you might imagine. They also dry very quickly (undoubtedly due to their highly-breathable nature) in a dryer rack (i.e. not tumbling) on medium heat.