This check already exists:
The problem is probably the 'parent node' setting. Plugins look for a 'parent node' setting ("plugin.nessus" by default) and will only add nodes/notes under it. This is to avoid inadvertently modifying your project structure.
So for example to have all your hosts created under a 'hosts' node
You'd need to change the 'nessus:parent_node' setting to 'hosts', and manually create your hosts under "hosts". Nessus will look for any existing hosts and only create new nodes if none are found.