This has nothing to do with AS and is an issue between OP and his employer.
Often, when businesses negotiate a discount, part of the discount is that they (or their TA) will handle all ticketing issues other than "day of" IRROPS and functions which only the carrier handles such as applying UG's. That is part of the bargain. It makes a great deal of sense for the employer and it is hardly a big deal.
If it is a problem for OP, he ought to take it up with his employer. Perhaps the employer will give up its discount.
Whatever Alaska negotiates with its tickets is on them. We certainly don't have any requirement to book them. If they negotiated an agreement with a travel agency in a way that hurts their frequent flyer, then yes, it's definitely their fault.
I don't have this issue with other carriers.