For AUv3 plugins, it’s a bad idea to create additional desktop windows. In Logic, transparent desktop windows will be given a magenta background as a security feature - this often looks out-of-place, especially for windows with rounded corners, because the corners get filled-in in magenta (relevant post here). If there’s any way of modifying your design to use a single window, I’d recommend doing that.
In terms of resizing, AUv2 plugins only support client-initiated resize (e.g. using a corner resizer) in Logic, but AUv3 plugins only support host-initiated resize (using the plugin window’s border). You could consider querying the AudioProcessor::wrapperType in your plugin, and using the result to decide whether or not to display a corner resizer.