Ford Transits also have these roof caps (22 on my HR 148 WB). The holes are threaded and are covered with plastic plugs, similar to the MB. They are useful to install racks, solar panels, etc. The issue and its solutions have also been discussed in the Ford Transit Forum. Most owners are doing preventative measures over any unused holes, as they can potentially leak if the paint cracks around them. I plan to use Dicor leveling sealant on my roof.
2019 Transit 350 HR Eco Quigley 4X4