Yes. RSRDC overwrites the TMO Flotillas.upc, as well as the CareerStart.upc files, which control what you see in the game at the main menu, as well as some of the sub-menus. As to the "duds" situation, there are two places in the game that control the duds. The first being the Main Menu, when you first start the game, under Options and Gameplay Options. Tick the box and you have duds in Single Missions, War Patrols, as well as the Multi-Player missions. When you start a career, you have to set those Gameplay options while in the Captains Office, when you are behind the desk. Click on the wooden radio console to your left, and you will get another Gameplay Options choice, which must be set for each Career that you might be running. So you could have however many careers running concurrently, up until you run out of computer hard drive space for the Saves, and each could potentially have different Gameplay and other options set for each Career. All of the Single Missions and other choices available on the Main Menu, run off of the Main Menu Options choices...
Also, each time you change mod configurations, such as going from Stock to Bubble's TMO, or from Bubble's to Ducimus's TMO, or add RSRDC on top of that, or when you go back to Stock ("horrors!!!") you should empty the Save folder, which is what the game runs off of anyway. You have to empty that folder though (C:\Users \UserName \Documents \SH4), so that the game itself loads the new mod configuration data into it. The whole structure is re-created when you run the game. It does re-set all of your gameplay options, including the screen settings, as well as deleting all of your Career progress... but it eliminates incompatibilities between mod changes.
