The scale car is what counts, so use the actual height...ITS actual height. But there's more to this. Don't forget to include the height between the nether rails and the bottom of whatever it is passing under. Further, think a bit ahead: I had no idea I would acquire a Trix GG1 with its pantograph. Well, I did get one, and darned if I didn't have to run it with the pantographs down because they simply would not enter my tunnel portals. Even a CPR wooden caboose, with it's very high stove stack, got jammed inside a low section of my tunnel.
My minimum height, and that's without running any double-stacks in the modern era, is 4.25". With that clearance, my GG1 with pantograph lifted will scoot under the obstacle overhead.
Not to side track this post, but. The Silverliner MU's, in tunnels the pantograph follows the wire which is much lower. The pantograph lowers so close to the roof that sometimes the voltage would jump to the roof, a bouncy ride or wire defect could cause it. These are some of the same tunnels the GG 1 used.