A client currently has one company. They have two buildings under that company, Building A and Building B.
Building A is owned by X owner, and we just set up his bank account. They want the rent to go directly to his bank account. So I want to set the operating account for Building A to be the owner's bank account.
However, I do not want it to be the operating account for Building B.

Can I set the Building's operating account but not set the company operating account?

Or else I need to make a new company to separate the two buildings, although I cannot move one building to a new company because the company has multiple buildings.

You can set the operating account on the building without changing it for the entire company. Whatever operating account is set on the building will always override what is set for the company.