A long Manitou on a 100mm frame: Two wrongs do not make a right. 😆
It’s not about travel, it’s about distance between axle to crown, both static and dynamic, and trail. Key here is your axle-crown measurement.
I’m running an Io with Marzocchi MX Pros at 100mm, which comes up pretty long on axle to crown length compared to 100mm Manipoo or RS forks. For example, a swapped a pair of 80mm MXes for a pair of Rebas at 100mm a while back on another bike and gained 4mm in total axle-crown length.
Measure the axle-crown on your Manipoos and work out the difference. I’d say 40mm is a bit much, but with 25% sag, that drops to 10mm. Handling will be vaguer, as Stormer says above. BEar in mind you won’t always be at 25% sag, either – there will be times when the fork is extended, which will make the handling squirrelly.
Check with Genesis about warranty as well; it’s unlikely to be covered, and the designers may also not have factored in a longer lever (ie fork) into the equation.
I’d also consider a fork that’s not a Manitou. Seriously. Get a second hand Marzocchi or RS from the classifieds. That’s what I did when I built up the Io last year.