When you pull funds from a bank account to pay a bill there are two tests: 1) Are the funds available? 2) Are you authorized to draw on the funds? The first question is entirely automated, but the second question is not. Many issuers limit the number and amount of payments from newly registered bank accounts to protect against the possibility that you are making an unauthorized withdrawal. Chase may simply be applying the delay to all payments to provide some incremental security and for operational simplicity.
This is not what is going on. I pay both my Citi and Chase credit cards from the same Chase checking account, and have been doing so for years. When I pay my Citi card, the card balance goes to zero instantly, while the checking account balance doesn't decrease correspondingly for a day or two. In contrast, when I pay my Chase cards, the card balance doesn't go to zero for a day or two, while the checking account balance decreases instantly.