After verification, placeholders are indeed not replaced recursively, I was misleading you, sorry about that!
If you go the fully custom dialog way, you need to implement your own UI system: Wwise does not know about your sub-dialog.
If you want to use the Wwise Authoring styled controls, the placeholders need to be directly created under the HWND passed by WM_INITDIALOG: either those are present already in the template identified by the ID returned in GetDialog, or you can add programmatically new controls in that initialization function, provided cannot are not MFC instances. You can also use the populate table to bind a model property to other types of Win32 controls such as text fields or checkboxes, and those will also be replaced at instantiation time to use the Wwise implementation.
The best compromise for you may be to only implement specific controls as custom UI elements, which can be MFC instances without any problem, and just use the placeholder controls in the resource template for everything else.