When I ordered my Pepe Spruce/Rosewood from Ukulele Source, they also ordered an additional one to sell just like it with one difference. I wanted an Ebony fingerboard (I love the look) and they ordered a Rosewood fingerboard. When they arrived, we played them both. I was lucky enough that Daniel Ho was in town for a workshop and he played them both, too. Everyone agreed mine had the better tone. These are identical ukes from the same batch, by the same maker, with the same strings, etc. All things being equal except the fingerboard (same Rosewood bridge- everything).
In the grand scheme of things it probably doesn't matter a whole lot, but considering the size of the uke (how small it is), and the construction of the fingerboard (likely glued to the top of the uke. Compass Rose does a Cantilevered neck that is unique and likely has less effect on sound), it does have some effect. Spruce is a very bright tone, so depending on your tone woods, it may have different effects.
This is just my experience. I am not a luthier and I don't have a lot of 1:1 comparisons, just this one. Hope it helps.