I'll keep this short and sweet.
spamassassin --lint -D < email_message_to_test.eml
 dbg: check: is spam? score=4.205 required=5
Which is an entirely reasonable score, it is in fact what I'm looking for.
spamc -R < email_message_to_test.eml
Content analysis details: (-0.7 points, 5.0 required)
Which is way to low!
Looking for why, and how to fix it.
SpamAssassin version 3.2.5
running on Perl version 5.8.9
No previous installs.
This is embarrassing. It appears that --lint always returns a score of 4.205, no matter what email I feed it. I was misunderstanding what --lint did, and since I was looking for something wrong I jumped on it.
Both answers make good points, and even though I'd love to delete this :) I'm leaving it up in case someone else wonders the same thing.