Update - having done more research I was worried about the additional drag that would be caused.Having read various threads on this forum about covers for bikes on a towbar bike rack, I can see that there are differing views on whether they are a good idea.
We have a T6.1 with an Atera towbar bike rike and later this year will travel from the south of England to Scotland and over to one of the Inner Hebrides by ferry with our mountain bikes.
My feeling is that it would be a good idea to get a cover, but will it obscure the rear lights of the van? (The bike rack has a tailboard with lights as well, but I guess the more lights visible the better).
I called the Roofbox Company (who sold me the Atera towbar bike rack) and they advised that bike carrier manufacturers advised against using covers on the bikes while on a towbar bike rack as the wind would create more force on the bikes, and the carriers wouldn't have been tested in this situation.
I then emailed Atera with the following question: "Could you please clarify whether it is a good idea to get a cover to put over the bikes while on the bike carrier to protect them from dirt on a long journey, and also to reduce temptation for theft of the bikes? I have heard conflicting opinions."
Their reply was: "Bicycles must not be covered while driving. This may cause excessive forces to act on the bike carrier."