I've got a pugsly setup as tubeless, running endomorph tires, typically I run between 8 and 12 PSI in the tires depending on the conditions.
Is there a significant difference between performance of presta vs schrader valves at these low pressures?
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As far as I'm aware, at these pressures, there'll be no difference in performance.
A bigger issue might be the rim. The value hole will be either Shrader or Presta sized and will either not fit a Shrader or be hard work to seal with a Presta.
As far as for the tubes I have used, schrader valves offer a less restrictive air passage, that is they create less resistance (less pressure) on the pump side. That means that for a large volume tire, to be used at low pressure, almost any pump or even a low powered compressor will be a little bit faster. For that reason in particular, I use schreaders in my DH bike (2.5 tires) and prestas in my XC bikes (2.3, 2.1 and even 1.8). I once used presta on my DH, but it took forever to inflate with a hand pump.
The biggest difference will be that schrader valves are more susceptible to dirt and debris. You don't need to leave a plastic cap on the presta valve, but you will definitely want to keep the plastic cap on a schrader. Since this is a fat bike, you're hopefully riding through some dirt and mud, so I'd go with the presta myself.