Archer will miss the first Test at Lord's, starting on Thursday, because he has been playing in the Indian Premier League with Rajasthan Royals, who reached the playoffs and were beaten by Gujarat Titans last week.
On Tuesday, England coach Brendon McCullum also cast doubt on Archer's availability for the second Test, which starts on June 17, saying he is having "a little bit of a break at the moment" and needs to be assessed.
Archer has faced criticism from some pundits and former players for not prioritising England, with whom he has a central contract.
Stokes said he understood the frustrations around Archer's unavailability but believes it's a sign of the times with the proliferation of franchise leagues around the world.
"A lot of the points that people would be making around Jof and that situation I think are to do with the landscape back when they were playing," Stokes said, in a nod to former players.
"It's completely different now. There's opportunities for cricketers now that there wasn't 10, 15, 20 years ago.
"Yes, in an ideal situation, it would be unbelievably great to have everyone who you want available every single opportunity. But it's not the way of cricket at the moment. There's so much more out there for players."
Stokes said England doesn't want to run the risk of losing talented players such as Archer.
"There is a situation where it could get messy and players like Jofra might not play for England again if you handle it a different way," Stokes said, "and that's not good for anyone.
"Jof, I think, has shown that he is committed and loves playing for England. Just because he's not available for this first test match does not change that."
