Do the screeners know to this? I'm willing to bet that a screener would deny you based on a name mis-match. What do the screeners know of EBCDIC?
As for TSA staff, it is important to realize that this EBCDIC issue is not a problem that only affects one airline: it affects almost every single airline, including all flag carriers that I know of. The airlines have a pretty tight working relationship with TSA; note that they send electronic messages to the TSA describing their customers when people book tickets and just before departure so as to give the TSA the opportunity to prevent them from flying. Given that tight relationship, I'm pretty sure that the TSA knows a great deal about the limitations of EBCDIC and has informed their staff about the limits of what a boarding pass name field can possibly represent.
Keep in mind that screeners will let you fly even if you have no ID on you.
Anecdotally, I've never had issues with tickets that had my partial name on them in the past either ("Matt" vs. "Matthew") although this may have changed now that TSA requires full names and birthdays (I always use my full name now).