Dear Mam,
yes, the employee has also rights to represent the company.... but as said by you also, they might not entertain an employee only, without the auditor/CA of the company... it might be true that you know much better than the external auditor... but A.O. needs auditor/CA of company for some other better purpose... which is different from the operations of the company..
anyhow, better would be to go with your auditor and take POA from the company on the letterhead and consult the whole matter with your CA before going in front of A.O.
And there is not much to worry in CASS... but as always advised by all, better be prepared and be alert always.. just be alert, no worries...
Best Regards,
CA Lovely Arora
ca.lovelyarora @ gmail.com