Wouldn't you have a maximum you are willing to pay for commuting expressed as a percentage of your compensation, rely on background/credit check to flag accounts for probable fraud for HR to look into, and fire people you found defrauding your company?

Also anyone willing to commit a crime to pad their paycheck is probably doing other nefarious things so they want to dig a little deeper besides? This would be so trivial to uncover in most cases I can't imagine this would be a big deal.