AS configuration and IO pin reuse

Yes, keeping DCLK inactive prevents inadvertent modifications to the AS memory, I think.

The pin placement rules related to AS pins should only apply, if the AS interface is used for AS programming in user mode, which isn't the case in your application. Possibly Quartus doesn't consider this different usage of AS pins, if so, you can dare to disable the checks by assigning a toggle rate 0 to the signals regarded as conflicting, if the AS programming is performed by the default SFL image rather than a SFL instance in your code.

I don't want to decide about your plans with ASDO in detail. I assume, there's a way, to make the load compatible.