Like you mentioned, the regular dining plan includes an entree, a dessert and a drink per meal, regardless of whether it's quick service or table service.
I couldn't see about some meal items or desserts not being included - all the restaurants I ate at, I could get anything I wanted off the menu. I know some restaurants are not part of the dining plan though, which you can verify in the restaurants section on wdwinfo or on Disney's website directly.
Basically, if you go to Pizza Planet, you get to pick your meal (pizza), your dessert (cupcake), and your drink. They will let you know if you're forgetting something - when I went to ABC Commissary, my aunt wasn't in the mood for a dessert, so we didn't ask for one. The lady reminded us about it, and when we mentioned she didn't want a dessert, she told us that we could get something else instead, like a bottle of water. Everyone makes sure you get what you payed for (or well, would've

)
The only meals I had that were different were the following: Mama Melrose on the Fantasmic dining plan allowed us one appetizer and one entree each, and then a dessert platter to share. Cinderella's Royal Table meal includes an appetizer, an entree and a dessert for everyone - I may be wrong, but I think this is the case for most signature/2 credit dinings. And then Chefs de France had an option of also getting a three course meal. If you chose to do that, there were select items that you could pick from for all three courses, mentioned on the menu. If you opted out of that, you would get your normal entree and dessert meal, and then you could pick whatever you wanted off of the a la carte menu.
In all cases, when we were getting something slightly different, the waiter/waitress explained it to us at the beginning of the meal
The credits are also on a per person, per nights basis. Basically, with the regular dining plan, you get 7 table service credits, 7 quick service credits and 7 snack credits. It is up to you how and when you want to spend those. You could do two days in a row of just eating table service meals if you wanted - all that would happen is after those two days, you would only have 3 TS credits a person left.
Also, though I cannot vouch for what you mentioned with certain meal options not being included, I am 100% that they will mention it to you. Every TS meal we sat down at, one of the first things the waiters asked us is if we were on the
DDP - even at Planet Hollywood in DTD