Hello Glen,
Thank you for your message.
Unfortunately, currently it's not possible to enable the 2-factor authentication feature only for one type of connection, i.e. if it's enabled then you have to use 2FA every time you connect to a remote Host regardless of the connection type. However, I'll forward this to our development department for a review to see if we can implement this feature in our future updates.
Sorry if this makes our software less useful for you.
Please let us know if you have other questions.