Can one payroll system generate BIR 2316, the EA Form, and IR8A in the same year-end run for a company operating in all three countries?

Yes. Omni HR generates BIR 2316 for the Philippines, the EA Form for Malaysia, and IR8A for Singapore, all from the same payroll data it's processed all year. A company running payroll in all three markets doesn't need separate software or a manual reconciliation step for each country, as long as the platform natively supports each one.