You might like to verify this observation and raise an issue with the GitHub project if it is indeed the case. It would be likely an unintended defect.
org-roam-buffer-toggle uses the same set of functions to display sections
(org-roam-buffer-render-contents), which in turn does this below to call section-functions to collect and organize the elements to display in each respective section.
(run-hook-with-args 'org-roam-mode-section-functions org-roam-buffer-current-node)
The unlinked references uses the title and all the aliases of each node by the look of the section function.
So by this casual observation, it’s hard to see how different sets of unlinked references are displayed depending on which alias you use – you may well be correct and my observation incorrect.
You can add your own custom function to the