Hi Thomas,
To be frank (well I can't help that) I haven't tried to do the inner only with added fly later bit, however I would say that it wouldn't be all that "easy" to do.
I have recomended before and still do to just set it up fly+inner leaving the door panels open.
Because the sides are very large you do get a good view and air flow just like that.
I am just back from a few days in the bush where my recomended set up worked really well because it was warm and humid and showers threatened every half an hour or so as the weather kept closing in and then lifting again.
I was in a spot notorious for that so there is no way I would have had the tent set up without the rain fly.
So this is what I am talking about :
photo stolen from the net because all of mine have at least one panel closed.
This is mine a couple of days ago :
we kept the two vestibule panels like that because of the passing dark clouds , it was however around 20c (68f) during the night.
If we had inner up only it would have not been any cooler (bugs were about…)
The next night we had no door panels in use at all (as in the top photo) but had partial closure in the late afternoon , still good enough for air flow and "views", in this case a grazing wallaby :
This is a closer view of the same fellow:
