The roof rack is an option on the SR5, but standard on the SE and Limited.
That's an awful complicated install for a dealer... I can't see the roof rack being dealer-installed unless the roof is pre-drilled at the factory. The dealer does put the crossbars together, but all that involves is sliding them into place on the rails and the installing the plastic trim pieces on the back end.
You need to find a dealer that knows what they're talking about here. Because it's an option on the SR5, then somewhere there is a part number for the rubber weatherstripping that would fill the slots in the absence of the roof rack. Your dealer was right about the holes, though - you'd have to fill them somehow (silicone?) before installing the rubber part.
Another source of info would be a body shop. They've got exploded diagrams of the whole truck with part numbers so that they can replace damaged parts. If you can at least get part numbers, then a Toyota dealer should be able to understand what you're talking about and order the parts.