To the OP:
DH & I also plan to not eat at any of the MDRs for dinner on our upcoming 3-night Dream cruise. We're leaving the teenagers at home (and school -- Bwaaaahahahaaa) and enjoying each other doing things we haven't before. We're eating our dinners at Palo, Cabanas, and Remy. DH finally got around to asking me what we do with the prepaid tips to the MDR staff since we aren't eating our dinners with them like we have previously. I told him I still planned to leave the recommended gratuities for them because even tho we don't eat dinners in the MDRs we enjoy breakfast and lunch options moreso than the buffet. That was a good perspective to present and it makes us both feel okay with paying those recommended gratuities. Of course we'll be tipping additionally at Palo & Remy. We accept all of this as part of the overall experience and customary way of doing things.
In a different thread I asked the question where do we take the gratuity envelopes if we won't be seeing our MDR servers on the last night or the morning of debarkation. We normally hit the buffet our last morning because we always select 2nd seating and don't want to wait that long to eat breakfast. I was told we could drop the envelopes at Guest Services the last night. I also asked if we needed to let someone know (head server?) that we weren't going to be dining at the MDR for dinner. I was told we could maybe let the CMs at the dining changes location during embarkation know. I don't want our MDR servers to go to a lot of trouble resetting our table for us only to have us not show up. Ya know?
They're good questions you have. I had them, too. I don't think you were coming off trying to be cheap or like you were trying to stiff anyone. Definitely felt like you were looking for clarification and sufficient reasoning to justify the cost. I know I don't like feeling as if I'm paying for something I'm not getting. I think you got some good info here. The recommended gratuities cover a lot more than just the MDR service at dinner.