First off just how much out of alignment are we talking about here? If the stabilizer is tilted only 1/4 inch over a 10 inch half span then it's not an issue. If it's a 1/2 inch tilt or more then it most certainly will be an issue.

You can always trim a model that is out of alignment to fly at ONE speed and in level flight. But it's when you want to change that speed or do maneuvers tha the misalignment shows up in some way.