Within the different types of taxes that apply, the tax law does apply a concept known as contra interest. So if you overpay and underpay, the interest charges and overages can be offset. They're offset on an even basis, so there's no differential there.
You're probably right that most corporations don't plan on leaving money on the table with the Canada Revenue Agency. That is appropriate, and it explains part of the impetus behind this measure. Most companies don't do that, for obvious reasons. If a company is looking for somewhere to place surplus funds, they can place them with a financial institution, in which case they would get a lower rate of interest than if they placed them with the Canada Revenue Agency. That's considered to be inappropriate. On the contrary, if a corporation goes out and borrows, they will pay a higher interest rate than they will when they place their funds.
Those are sort of normal business realities. They also apply with the CRA and the amounts the tax law requires they pay and charge in respect of overages and underages of tax payable.