Of course it was a blow and he is indeed their third rider in pecking order right now. I would still expect he gets the freedom to choose Giro over Tour if he believes he is incapable of defeating Vinge/Pogi.But then comes the question: we can speculate as much as we want: what does Roglic want?
I personally think this whole tour is a blow for him. The tour was his one an only goal in cycling still to be reached.
He is now not only pushed to the second Gc spot at jumbo, but will also be after Wout within the team hierarchy,
The wholy dynamic will be different I highly doubt Primoz will be at a GT with Jonas ever again.
I also expect that if he turns out in better form than Vinge on TDF he will get his chance to win the race. In 2018, he was not their TDF leader (Kruijswijk was) but was protected rider and he got enough of support to beat Kruijswijk in the end. They even saved him from certain GC doom in crosswinds stage...
So everything is not as bad for us (or as good for you) as it seems. A lot still depends on your current from and if you have the legs, things are a lot more simple.