In general, that’s correct, default avionics (G1000, FMS, etc.) will use Custom Data if it’s present, replacing the default data; or, the default data if that’s all one has. Some third party addons with custom navigation systems will make the same selection, however will be reading the data directly from the disk (rather than through X-Plane’s programming interfaces, which are quite crude).
However, the CL-650 is the only addon (that I know of) that lets you select either the default data or custom data while in the cockpit. That’s the key differentiator here.
In theory it could be implemented so that the two databases could be read from arbitrary locations, including outside the X-Plane directory, however that’s not the design choice that has been made at this time.