Anytime light moves from one medium, such as air, to another, such as glass, it refracts. In theory, when the glass surfaces are parallel the shift is back to the original path. My concern in putting glass over the paper for enlarging would be whether the glass surfaces are perfectly parallel, or how imperfect they might be, and whether the surfaces are in perfect alignment with the lens, which almost certainly, they will not be.
Whether those imperfections are enough to matter for your eyes is a different issue.