The likelihood that they stay together for the next three years, that they both decide to pursue PhDs, and that they are both accepted into PhD programs they want to attend . . . probably adds up to less likely than that they stay together for another x years after all that happens.
So, yes, it’s not that likely that they have a future together if those are really their plans. Don’t tell them that; let them find out for themselves. Also, give them the opportunity to make different choices if the relationship is really important to them.
For some examples:
I am friends with a youngish couple who started dating in college. They both wanted to be English professors. One got his PhD at a top-5 program. The other got her PhD at a second-tier public university in the same city as the first one’s prestigious program. The one with the prestigious degree has tenure at a mid-level public university. (In that field, any kind of tenured position is fabulous.) The other is a part-time contract instructor at a small Catholic college in the same city. They are wonderful people, they have three great kids, and they are very, very happy.
My wife and I were friends in college, but didn’t get involved romantically until just after I graduated. I was a year ahead of her, and headed to law school in California. We wrote lots of letters that year. When she graduated, she deferred any graduate school plans, moved to California, and started looking for jobs. A year later, she applied to the Kennedy School and was accepted, but I got a job offer I couldn’t refuse in Washington, and she decided not to go to the Kennedy School. Instead, when I went to Washington, she went to law school in Philadelphia, notwithstanding that she had established California residency and could have gone to Berkeley practically for free. After a couple of years in Washington, I moved to Philadelphia and we got married. At the time, we were planning to move back to California when she finished law school – she spent the summer before our wedding working in San Francisco – but then she changed her mind about what she wanted to do, and ended up accepting a job in Philly, where we have lived happily ever after.
When she was in college, my daughter was close to a PhD student at her university, which was in Chicago.The PhD student was involved with a guy she had met in college. For a few years, they lived about 1,000 miles apart, she in Chicago and he near Boston. Then he got accepted into the Iowa MFA program. At that point, she had basically finished her coursework and was working on her thesis, so they got married, and she could live in Iowa City 4-5 days a week and come to Chicago for a couple of days a week. There were a couple of years in there where she was teaching someplace else every semester, and he taught at a boarding school in New England, but she finally got a tenure track job at a fine university, and he got hired as a writing instructor there.
In other words – people can make things work with some flexibility, some compromises, and a willingness to make some career sacrifices for the relationship. That’s OK.