Is a 25" tall cage for a dog 21" at the shoulder is ok for car travel?
I know its not ideal for airline travel etc, but it means he can stand up but not raise his head? He travels lying down
I'm loath to make it bigger (is for fitted cages) because the top is already 22" for a 17" bitch?

Well yoru alowign the smaller dog 5 inches above with3er height and only 4 inches for teh taler dog. 

If your building them in I would go for at least 26 inches for the bottom one and that woudl still give 4 inches clearance for the smaller dog, which arguably needs a smaller proportion of headroom, if you get what I mean. 

4 inches is a smaller proportion of 21 inches than 5 inches is of 17. 

5 inches as a proportion of 21 inches is 23.8%, and 4 inches of 17 is 23.5%, which seems more appropriate than the above which would be 19% and 29.4%.