Owner of ABC, LLC comes in to bank and makes $20k cash deposit into business account, the biz name goes in Section A, owner's name goes in Section B...is box (e) in Sect B checked as well (Conducted on on Behalf)?

I would not.

Agree.

And when would it be appropriate to check that particular box?

One example would be in the case of a dba.

Or if I make a deposit into my own account as an individual.

But if an entity is the only person listed in Section A, it clearly can never complete a transaction on its own behalf.

Yup.