On my 2003 Explorer, that body style was notorious for low voltage charging from factory. I had 3 alts, the factory one, the a re-made factory one at 180 amps, then my 300 ext vol regulated alt. My car computer would be lucky to chage at 14v. A lot of times it would fall to 13.5-13.8v, iirc. The rebuilt factory HO alt helped, but it would still not charge that high. I would charge at 14.8v-15v with my 300 amp ext vol reg alt. They can be a pain, the regulators.
Your alt will still put out power, just having the car computer control the voltage, it may very well affect or lower the charging voltage of your new alt. You'll just have to see. As long as the alt is charging under a load, I wouldn't worry about it too terribly much, unless you want it exactly how you want it.