The schedule already has plenty of padding. It just isn't enough to account for the unprecedented weather delays it's experienced this year.
Additional time added to the schedule:
1) Would be almost impossible to take out once the conditions improve (host railroads don't like giving up time once they get it)
2) Would break connections, hurting the train's revenue
3) Would increase crew costs, possibly breaking operating crew turns which would drive up costs even more (and would require hiring additional conductors/engineers, which would take months to train and qualify)
4) Would possibly require additional equipment, depending on where the padding is added.
Meanwhile, Monday's arrival into Seattle was less than 20 minutes late (Portland was less than 10), so I'm not sure what additional padding would have done to that train other than to increase costs. The train has been doing quite a bit better eastbound, too. Monday's Chicago arrival made every connection except for train 370 (9 passengers), and would have even been in before 5 pm (thus making that connection) except that it missed a Metra slot by about two minutes, and had to follow the local all the way in.
Your description of the Empire Builder's OTP is very simplistic and not reflective of the reality that the Empire Builder has historically encountered.
The FY2010 OTP was 78%. Its OTP for September 2010 was 82.5%. That doesn't really match your doom-and-gloom description of all these things that "often cause the EB to be late."
I mean, "Autumn: derailments and other miscellaneous things..." That's a ridiculous stretch if I've ever heard one. Derailments can happen on any line, at any time. Do you have any real proof that there are proportionally more derailments on the Empire Builder route than anywhere else in the Amtrak system?
You throw the term "slow orders" around, but, other than around Devils Lake, what slow orders are you specifically talking about? Snowbanks? Seriously? Avalanches...not too common, but yes, they can cause disruptions if they occur (and "padding" won't fix a disruption caused by that; you're either going through or you're not). Mudslides are a problem on the West Coast, but those do not impact the train's OTP. Instead, they just determine (generally) whether the train will carry passengers past Everett.
Finally, I must take exception to your only "No" option being "No, misconnecting passengers and other OTP-related issues are insignificant." Those issues are not insignificant, but, other than this year, they really have not been a problem for the Empire Builder (at least, not moreso than any other western long-distance train).