What does 2FA authentication have to do with shady devs?
Because shady devs apparently have been hacking into the Developer Portal accounts of stupid devs who use weak passwords. This enables them to obtain assets needed to re-sign the stupid dev's apps with their own Enterprise signature.
Some shady devs might even hack into GitHub, Bitbucket, etc. to obtain actual source code. Of course, Apple has no control over that.
Honestly, there is NO need for 2FA so long as strong passwords are used, and rotated on a regular basis.
If you are using 2FA, and not offering the use of a hardware security device (dongle or keypad-equipped appliance), you might as well not bother. Apple does not to my knowledge offer this option.
The device has an accurate clock. The login server (or some hardware device attached to a login server) has an accurate clock. After providing user ID and password, the server challenges the user to provide a one-time code. The user punches a personally-selected PIN into the device. The device provides a one-time code. The code is typically good for one minute or so. An algorithm present in both the device and the server (or some device connected to server) is able to generate the same one-time code based on current time and security device ID (each is of course unique) and the codes are compared. If an account might be shared my multiple individuals, multiple security devices would have to be registered. Typically, these are small devices that people carry on their physical keychain.
MOST banks offer this option and typically provide the appliance for free for large accounts. They only cost a few dollars, in any case.
I will have to review, there was a notice from Apple when last I logged-in to the developer portal about changes in how linked accounts are handled. I *think* this might be related to some mitigation of the need to ever actually log-in to a company account after initial setup, assuming sufficient privileges have been given to linked accounts. Will go read when I have time, obviously soon!