@murgatroydj what kind of issues are you running into?
Dev mode shouldn’t be dependant on the DB prefix side of things. Providing some examples of what you are running into may help discern what layer of caching may be taking place.
@murgatroydj Hopefully it’s as simple as what I just discovered on my local copy. Custom setups do not have that option as it doesn’t use the Varnish setup which is where that Dev mode option comes into play.
If the sites that cannot be enabled is not currently running, once you start it up the option should allow you to toggle.