At least in my experience, credit union IT departments aren’t exactly crackerjack organizations. They outsource their online banking platforms to third parties and quality varies widely. Certain institutions (First Tech FCU and Keesler FCU come to mind) are more fickle than others.
You are correct that bill pay is outsourced to the same group of vendors, but the individual deployments of each banking platform still need to talk to them. As APIs are deprecated or as breaking changes are made to these platforms, are these smaller banks telling their vendors to test and update their individual deployments?
Further, again, many of these smaller banks will have varying rules for funds delivery time, and some charge a fee to use the bill payer. It’s just easier to initiate an ACH pull at a larger institution rather than incur an unexpected fee or risk violating “Argyll’s Rule” because certain banks hold funds for a few days before they forward the cash on to the biller.
Ally is big and predictable. That has its downsides but one of the benefits is that there are plenty of data points on what to expect in terms of their feature set, bill pay included.