Just to follow up on this one...Although I haven't fixed it yet I do have the part number
Part # 002 998 0250.
The plan is to remove old cap, clean area with acrysol (recommended by Peter at SMB West), Sikaflex 221 and install cap, replace tape across the roof where the penthouse top lands and ensure that the shims inside the van continue to keep the ceiling material from pushing up on the cap.
I used Dicor self-leveling (black) sealant to cover all these caps on our Transit roof. It also comes in white. It’s the sealant that many people with RVs use on their roofs. I’m sure that Sikaflex would be a reasonable alternative but I have no experience with it.