It’s a common refrain these days: Let workers decide where and when they work.

The impetus, of course, stems from the pandemic, when employers sent office workers home for a year and a half, with surprisingly few hiccups. Productivity didn’t suffer, and workers enjoyed their newfound freedom. Now, we’re told, companies can’t go back to the old, controlling ways without workers revolting.

That may be, but here’s what almost certainly will happen if the hybrid advocates win the day: Companies will have a two-tier workplace, with on-site workers getting the bulk of the promotions and raises.

Why would that be, especially after we’ve apparently just seen the benefits of remote work? The reason is simple: The experience during the pandemic was totally different from the circumstances going forward—which means that the pandemic past isn’t a reliable guide to the pandemic-free future. For one thing, during lockdown, workers had a sense that they all had to pull together to keep their businesses afloat (and their jobs) and bosses were willing to let workers decide what to do and when. But the biggest difference between the pandemic practices and the hybrid arrangements we are considering is that in the former, workers had no choice. Everyone who could work from home did work from home. By contrast, in virtually all the proposed hybrid approaches, employees choose whether they are in or out of the office.

To understand what that means, just imagine that you and your friend are doing the same job at roughly the same performance level, but your friend decides to work from home while you decide to return to the office. No prizes for guessing which of you will get ahead.

Unfair but true

There are many reasons why this will be so, even if we believe it unfair. There is, for starters, human nature: If I’m the boss trying to sort out candidates for promotion, I’m looking for signals of who is more motivated and who is more committed to the organization. You put in the effort to be with us in the office, your friend doesn’t. It may be a biased and unfair signal of motivation and interest, yet it is one that most leaders will find hard to reject. Unless an organization is terrific at managing performance carefully and objectively—and few are—face time still matters.

At the same time, employees in the office get more access to leaders, who likely will be in the office most of the time, even in hybrid situations. The on-site employees get first crack at opportunities that pop up, because they are likely to see them first.

Another difference for remote workers is that they will now likely be a minority beaming into meetings. With good video, it won’t necessarily be the same as it was when “calling in” on a speakerphone meant that participants in the room forgot about you, but you will still be the odd person out. If the video screen is too small, you likely will be ignored; if it is too big, your face will be subject to intense scrutiny. Even a small lag in your transmission becomes jarring when everyone is talking face-to-face. Technical glitches are no longer so understandable if you are the only one having them, and it isn’t so cute when your dog starts barking on the video now that everyone else’s dogs are quietly at home.

It is also a challenge and arguably more work for supervisors to manage remote workers. It requires more scheduling for checking in and more intelligence-gathering. And it will mean more running interference for projects of remote workers who cannot do that as easily themselves.

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Look at it this way: When supervisors have one group in the office and another group working at home, they have to operate two different systems of management. Will they be able to do both and keep them straight? If not, the default is likely to be the in-office approach, for the simple reason that managers know it better. Once again, the remote workers will be at a disadvantage.

Objective outcomes

There are two likely rebuttals to these concerns. The first is, let’s just make sure that supervisors at all levels focus on objective performance outcomes so that it doesn’t matter whether we work from home or not. This will be reinforced by potential legal issues. Anytime we have two groups of otherwise equivalent workers doing the same jobs but we are treating them differently, it’s an open door for legal challenges. Say that remote workers have lower rates of advancement than those in the office. That might not matter if the two groups were identical, but what if women with children at home make greater use of working from home? Do we trust our performance measures to defend against charges that the different career outcomes are due to gender differences?

Still, most organizations struggle even to do the most basic performance management, such as conducting effective performance appraisals. Getting them to eliminate supervisor judgment and biases is frankly an impossible task, especially in administrative roles where work products aren’t easily measured.

The second rebuttal is that the situation will be different if we have only occasional work from home, so the differences between in-office and hybrid won’t be all that great.

That may well be true if everyone takes roughly the same amount of time at home. But that is extremely unlikely. The central demand from employees is to have choice, and employees vary considerably in their interest in remote work. Social pressures, individual circumstances and work norms all affect the likelihood of using work-from-home options, as we have seen with the related practice of vacation time, where less than half of U.S. workers use all the time they have earned. The same is likely to happen with work from home.

There are actions that might help reduce the two-tier outcomes of remote work—such as explicit statements from leaders that work from home is perfectly appropriate (unfortunately a 180-degree change for many organizational cultures), training for supervisors on better performance management, and so forth.

Even with the best of intentions, though, it’s hard to imagine a system where we won’t end up with two tiers of workers. We don’t want it to happen, and we don’t want to believe it. But we need to go into this grand experiment with our eyes open.

Dr. Cappelli is the George W. Taylor professor of management at the University of Pennsylvania’s Wharton School, director of Wharton’s Center for Human Resources, and the author of “The Future of the Office: Work From Home, Remote Work, and the Hard Choices We All Face.” Email him at reports@wsj.com.

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