A HBC wad wouldn't work, and that's why you can't find one. It has built-in checks to see how it was installed and refuses to work(or at least work properly?) if you did not use the official installer.
Dolphin should emulate all IOS slots. I thought if the running software says: "please start IOS x", Dolphin waits a few moments and then reports: "there, now IOS x is running", without actually loading that IOS or even checking if it exists. So in theory, if an usb loader wants to load IOS249, it should say that it's using IOS249, but that doesn't mean anything. Well, i guess this still isn't right, because it doesn't match what is happening for you. But if software actually checks if the IOS exists, before loading it, you need to have it on your nand, even if it's not actually used.
Dolphin should emulate all IOS slots. I thought if the running software says: "please start IOS x", Dolphin waits a few moments and then reports: "there, now IOS x is running", without actually loading that IOS or even checking if it exists. So in theory, if an usb loader wants to load IOS249, it should say that it's using IOS249, but that doesn't mean anything. Well, i guess this still isn't right, because it doesn't match what is happening for you. But if software actually checks if the IOS exists, before loading it, you need to have it on your nand, even if it's not actually used.