Well, to answer my own question if anyone else is curious the answer is yes. You can add on-board credits through WDW and bypass your travel agent if you booked through a T/A.
DH and I were debating prepaying our $400 CC cabana, but we decided not to. In case of inclement weather preventing us visiting CC, we did t want to wait for DCL to reimburse us for that expense. We put cash down against our KTTW cards at WDW once and didn't spend as much as we anticipated. The refund took two weeks to arrive.
I will point out that if anyone uses the Disney Visa, pre-paying to your onboard account qualifies for the 6-mos no-interest offer while simply using your Disney Visa to pay the onboard account will not. You can pre-pay any amount, it really doesn't "pay" any specific item(s) but rather puts a credit equal to that amount on your account to offset the charge once made.
I believe you can pre-pay to your onboard account up until 3 days prior to sailing, possibly even closer. But that 3-day mark is when the cruise is pulled from online viewing and a lot starts to happen behind the scenes.
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