The difference between 2D and 3D MID is that the last supports 3D secure transactions.
The 3D secure is a security protocol that works as an additional fraud prevention measure for online payments. It allows customers to create and assign a password to their card that is then verified whenever a transaction is processed through a site that supports the use of the scheme. The addition of password protection allows extra security on transactions that are processed online. The scheme is a collective of Verified by VISA (VBV) and MasterCard Secure Code (MSC).
After the 3D MID is activated, our system will check ability to follow 3DS flow for the card and send the transactions to the 3D MID. The users will have to follow the 3DS flow to complete the payment. The bank issuer will recognize this type of the transaction as an additional level of protection which will most likely prevent chargeback from happening.