I scoured all the Cocorahs and WU stations that are within the vicinity of LNS, THV and MDT, and they all seem to be pretty much in line with the totals reported at those sites. I think the NWS sites just happen to sit in localized spots that weren't hit quite as hard. It happens. We also aren't talking about much of a difference. They are all still over 3" and LNS isn't far off from 4". Chalk it up to randomness, me thinks.
As for evaporation with manual gauges, I've actually tested that out and found that's it's virtually nonexistent. I'm talking hot full sun summer days where I've purposely let the water sit in the gauge for days on end, and the amount lost is negligible. I think it has to do with the gauge being mostly enclosed at the top and there not being any easy way for the water vapor to escape, which may be an added benefit of the funnel design. Have I spent too much time thinking about the design mechanics of a weather gauge? Yes. Am I a weather weirdo? Also yes.