The margin may be better for Silver's, but I doubt it for any of the other levels. Assuming DL is getting .01/mile from AMEX, the waiver is only generating $250 for DL. Plus it adds a liability of 25K miles (or more) to the books. I believe the waiver is likely due to the total value of the AMEX relationship and has little to do with the amount of income it actually generates from individual Medallions. Given that DL and AMEX just recently renewed their relationship, I'm going to bet that AMEX has contractually embedded the MQD waiver and agree that it is unlikely to go away.
"Only?" $250 is a lot when you consider there's little to no cost involved. An FO making exactly the $3K MQD for next year probably made DL on average $150 in profit. Now suppose that somehow the FO qualified on MQM but spent $0 MQD and qualified on the waiver instead. DL still made $250 in almost pure profit. Now consider the most realistic scenario, that the FO missed and made say only $2K MQD but qualifies on the waiver. That's (on average, roughly) $200 in flying profit and $250 from the waiver. That "only" $250 means a lot in context.
I could see the required waiver amount going up, or being set higher for higher medallion levels, but it makes DL $$$ hand over fist and isn't going anywhere.