Once MTNet interfaced to application system the access point of the latter shall be closed and you are required to log in MTNet before accessing the application system. 

Certificate IC card is unique and held by you. No one else can use it to access MTNet by forging your ID. 
Login with certificate card would be the safest approach. 
Once your account/password is known to others, it may be used by someone to access the MTNet website.

The Citizen Digital Certificate functions the same as account ID and password in MTNet.

That is, just log in with account ID and password if without Citizen Digital Certificate or card reader. 

Please be reminded that it's much safer to log in with Citizen Digital Certificate when accessing MTNet on shared public computer.