Center channel
Most center channel speakers are not designed to mount vertically. It has to do with the horizontal vs. vertical dispersion pattern of the speaker. You don't want much vertical dispersion from the center (mounted horizontally) otherwise it would bounce off the ceiling and floor.
Also, since, you are building a custom cabinet, make sure it will fit an upgraded Paradigm center channel. It is very important to have a tonal match between the front and center channel. Finally, mounting any speaker in a cabinet, especially a ported design, will effect the performance of the speaker. Leaving the back off of that section of the cabinet might minimize the effect.