Hi gowthamtalluri,
I have repro your issue. I tried to add 2 queues , one tracking primary mailbox and another for secondary mailbox(Alias Mailbox).
And I sent mail from primary mailbox to secondary mailbox from Outlook. And the mail is only tracked in primary mailbox queue regarding Test3 pic
I also tried to send mail from another domain's mail address to secondary mailbox. While the mail is also tracked into primary mailbox queue regarding Test4 pic.
So I consider if anyone sent to secondary mailbox(Alias Mailbox) , D365 will consider the mail is sent to primary mailbox which could only be tracked by primary mailbox queue.
Test3:

Test4:

Primary Mailbox Queue Result:

Hope the above info could help.
Regards
Johnny