There's no gap in this.  The company takes the deduction based on 100%.  80% is attributable to business use and the remaining 20% to benefit costs of the shareholder-employee.

For W-2 reporting purposes, a different set of rules applies to the valuation of fringe benefits.  The business would determine the reportable compensation based on ALV unless the cents-per-mile rule is permissible.  Note, however, only maintenance and insurance costs are baked into these imputed amounts.  If the business paid for other expenses related to the shareholder-employee's personal use, those expenses will need to be accounted for separately.