things like car rental confirmations and airline reservations are marked negatively because they 

• Plan Text or Html message is base 64 encoded  (60)
• Body contains unnecessary character encoding (30)
• Email contains a web bug= ... allowing the sending to validate recipients email address (60)valot
• Bayesian Analysis suggests there is a 98% chance this message is junk (68)

other emails like for airline miles people sign up for are getting marked negatively for having works like EARN in them.

how do we make this less likely to mark these legit messages from companies so negatively?

I have the same problem. I use SendGrid to send my emails, and SendGrid adds some code to the email in order to know if it has been opened.

If a recipient then answers the email and chooses to show the content of the mail being replied to, Xeams hits the Email contains a web bug = 60 score.

We need a way to allocate the score value if this happens

Wouldnt the easiest solution be to just add these domains to your whitelist - ultimately SPF would still need to occur for the mail to come through giving you spam protection.

James.