So in the past 10 years or so, I would guess that I have either applied for, or bought bonus points for 30 or so quota permits/licenses/tags in a variety of states. Elk, moose, mule deer, antelope, turkey. And in each case there has been an application deadline that I could either submit by mail or online. My choice. Except for one of course. PA anterless tags which do not have a deadline but instead is like a bunch of runners in a track meet all at the same starting line and take off when the starters pistol fires. The solution is really easy. Declare a deadline. Mail or online apps accepted by that date at the choice of the applicant. Pay by check, money order, credit card, paypal, whatever. Leftovers go into a secondary draw with its own deadline or become over the counter. If you lose the first draw then you settle for 2nd choice. Maybe there is a good reason why everyone else does it the other way.
The connection to the county treasurers is a remnant of the old county by county anterless quota system. With that no longer the case, it's hard to make a logical argument to keep the counties involved. And like others have said, why should the county treasurers feel entitled to these funds.