Actually, the study included two more diseases than the ones I mentioned (hepatitis B and one I never heard of).
But the thing that puts the number way up is including HPV — it has a decades long latency period during which there are no symptoms, but it can be passed on, is not just sexually transmissible (besides vertical transmission from mother to child, there are documented cases of transmission by sharing clothing in the medical literature, and unlike every other STD, clinically significant viral loads can be recovered from surfaces in public restrooms — it may be the only STD for which the old lame ‘I must have gotten it from a toilet seat’ might actually be true, though unlike the transmission by sharing clothing there are no documented cases of this), being viral it is never cured (though it’s usually asymptomatic rather than actually causing genital warts, unless in women it causes abnormalities in a pap smear or, if not caught by that, cervical cancer) and (also unlike other STDs) the very high transmission rate during sexual activity is not decreased significantly by condom use.
Pretty much everyone who’s ever committed fornication, and even a lot of folks who saved themselves for marriage and have been faithful ever since have HPV.
The study is behind a paywall from a commercial scientific journal, so I couldn’t see what the numbers would be if you excluded HPV. I suspect those numbers would be much closer to the intuition you have that’s causing your disbelief.
The people in the second group have this little health problem because they married someone from the first group.