Whether the difference between a 100mm and 90mm stem is significant can be a very individual thing. Due to an old neck injury and permanent C2 damage, it doesn't take much of an adjustment to make the difference between comfort and agony. I make lots of very minor fit adjustments to suit how I feel, or as my flexibility improves (or, in some cases, deteriorates due to inactivity caused by illness and injury).

A stem with reduced reach could also be more aero and still comfortable by lowering the stem/bar a bit. I was able to do that by switching from a long stem to shorter stem and lowering the bar.

But that gets into a whole nuther realm of marginal gains, as Team Sky described it. I'd go for comfort first. That alone can improve speed or endurance over distance just by reducing factors that cause fatigue.