After reading the Rep's quote, I am convinced that he mispoke or had a case of "fat fingers" on the computer. Makes more sense that a failed part would not be covered under warranty if the battery were NOT disconnected. Just think....what is one supposed to do when the vehicle's battery must be changed due to age or an internal battery problem still covered by the warranty??
Suggest you follow the Owner's Manual since it is the base authority for such things. As a former automotive manufacturer factory rep, I know all too well that even reps make mistakes....they are, after all, humans. And most of us are/were not electrical engineers. God knows I made my share of mistatements....still do! Take care....
2003 Fleetwood Revolution DP