No matter how you want to argue it, the concept of "fly now pay later" requires exception handling, and that costs money.
It's been my experience that most airlines outside of the US issue an ID00 ticket for travel. That allows all of the normal processing to take place with regard to issuing a ticket, proper collection and calculation of taxes, etc.
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When AA went with ticketless D2 travel back in '94 and eliminated the old yellowish Form 45 "Write Your Own" paper tickets, I headed up that project. One of the options we looked at was advance payment for all service fees, particularly for D3 to get rid of cases where employee paychecks were getting wiped out because of the fees and taxes. It obviously didn't happen, but that being during the Crandall days, we looked at every option (regardless if it was politically feasible) before just acting.
Sabre is the surviving Res & check-in system, so the need to change here isn't an integration issue. All of the associated infrastructure I put in place still exists (post-travel pricing, tax tables, and hand-off files for the billing processes).
The cost of building all of that was paid off over 15 years ago, but the cost of maintaining it continues.
Nonrev travel at AA used to drive about six heads -- one to manage all of the airport and industry mandate issues (policies, jumpseat agreements), one head just to handle abuse investigations, one head in interline to manage OA agreements and issue OA business pass requests for travel on AA, and another three heads to deal with all of the pricing and billing. Back then, the automation budget for maintaining the tables and jobs needed to do all of the billing was in the six figures for Sabre to maintain.
All-in, it was costing the company ~$250K to administer what is considered to be "free" travel.
If the company wants to look at saving that $250K (not adjusted for inflation...), then it's their call to do so. Moving towards the way US did it isn't an unusual way of managing employee travel. It's just different for the way that everyone else in North America is used to seeing it managed.