I’m not exactly sure what 6 digit code it’s referring to. I never set up 2 step verification so there’s no way it could be that. Is there some other code related to Google Drive, and if so, where do I find it?
It’s been a while since I set that up for a test. The first time I tried I received the same thing. I believe going to the account there was a message for me to allow LibreOffice access. Once allowed, it never asked for that code again. Currently have two accounts set & recently re-tested without problem using LO v5.4.1.2. LibreOffice is now listed in the Google account under the setting My Account -> connected aps & sites.
Edit:
Did some testing today. Deleted my LibreOffice ap on Google & signed out of Google account. Tried to access using remote files. After initial password, it asked for the 6 digit code. Canceled it. Back to Google account. No message. No way to add the ap back in. Left the Google account open and again tried to access using remote files. This time after initial sign-in it did not ask for the 6 digit code. Signed-out of the Google account & subsequent access to remote files worked & never asked for that 6 digit code.
Long story short, first time access from LibreOffice have your Google account signed into and open.
If this answers your question please click on the 
(upper left area of answer).
Please see Unable to connect to Google Drive, LO 5.3, UBUNTU 16.04 answer - edit portion. Found 6-digit number.