I’m a little surprised that MVC/LA at OP’s school only gets the 4.0 weight. At my kid’s (private) school all post-AP classes get the same weighting as the AP classes.
MVC/LA is probably not going to be very rigorous in any high school, but will still be tougher than AP Stats. If the only reason for not taking MVC/LA is the grade weighting, I think it’s a no brainer to take MVC/LA. It’s not going to help much for college admissions, but it won’t hurt either, in both cases for an otherwise 4.0 student. Even previewing linear algebra in HS will have some value for a potential CS (or biostats or bioinformatics) major.
Even if the MVC/LA course is unweighted, the minor GPA penalty on the weighted measure is no big deal imo, even though it would likely knock him out of the running for valedictorian. No one will know who is valedictorian until well past college decision time - and just about no one is going to care even a few weeks after graduation day.