Ignacio,
Try making your roof pitch within the range suggested
in the pop-up message then, place all the roof windows
that you want, then change the roof pitch to what you want.
I don't think you will get the pop-up.
I know it's really dumb but it seems to work.
I also notice that, unlike previous versions of AC,
the plumb cuts at the eave and ridge stay plumb
after the pitch is changed from the pitch assigned to the roof
when the roof was first created.
Which helps this dumb work-around work.
(Is that a complete sentence?)
Peter