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I don't think they underestimated it, just that there wasn't really anything they could do to counter it. As soon as Hamilton pitted there was a message between Max and his engineer saying "This could be another Hungary" referencing 2019's race where the exact same thing happened (Verstappen leading, Merc/Hamilton having the faster package, pit Hamilton who comes back from a 20 second gap with fresher tyres to take the win). Red Bull would've had to bet for some pretty bad luck with Hamilton's stop or out lap to not have him undercut Max.
Without a rear-gunner Red Bull are always going to be on the back foot relative to Mercedes when it comes to strategy. If Perez was where he really should've been, Mercedes would've been a bit more hesitant to go for that strategy. Though to be honest, I imagine they would've gotten the win regardless, probably just would've had to fight a bit harder for it.
mmccarthy-
As well as Perez, Red Bull really need another team to be fighting for podiums as well. Stealing some of those podiums and points from Bottas so Mercedes don’t walk away with the constructor’s championship. The commentators (critics?) give Bottas a hard time, but they forget he’s securing the constructor’s championship by consistently bringing those points in.
Jonny69
After Hamiltons second pitstop I expected Red Bull to pit later but go for soft tyres. I think they underestimated how much Hamilton would catch up and missed the perfect timing.