I don't know that I'd call it a shell game. If you wanted to accurately assess differences in flight time between civilian and military applicants, and you placed a premium on flight time by itself, then it makes sense to ensure that the time is logged in the same way or that you make adjustments for differences. How one makes those adjustments and how much emphasis you put on flight time as a hiring criteria is certainly up for debate.
Airlines and large fractionals do a lot of data crunching before they send out interview invites, and they are the ones that generally make these adjustments. Smaller operators with smaller hiring requirements can probably do it on the fly from the raw numbers. Quite frankly, I don't believe that flight time (past a minimum point) is an accurate indicator of potential performance and would be more interested in how they got those hours and the job applicant's technical knowledge, temperament, and attitude towards compliance and safety.