Put it this way; for the sake of argument, let's say US wants to admit Puerto Rico as 51st state. And although rape in US is illegal, under "popular sovereignty" doctrine, we gonna let Puerto Rico to decide if they want to allow rape to be legal in their state. Hey, it's their business, right?
Uhm, no. Those who are anti-rape, will not allow them to join the Union. And those who would let them decide about rape being legal... they're not really against rape, are they?
Bad analogy. Rape is not only already illegal in Puerto Rico, as it should be, but clearly an act of violence that was never legal anywhere. Popular Sovereignty meant something like what happened in Bleeding Kansas. It was obviously a bad idea simply because of the lengths the partisans would go to, as demonstrated. Kansas showed that leaving it up to the states wasn't going to work and stronger federal law would have to be applied to the question. Kansas in fact represented a microcosm of the War that followed it, and should have served as a warning. The Democrats' fault was in holding too fast to the position of smaller central government and "states' rights". That's (again) why Buchanan couldn't stop the War --- he was conservatively mired in that "states rights" position and unwilling to expand the power of the federal government.
It's not bad analogy, but your bad reasoning.
I know rape is illegal in Puerto Rico, that's why I said "for the sake of argument, let's say..." If you're not able to process that little, why are we talking at all? What if we replace "rape" with let's say "abortion"? For the sake of argument let's say that Puerto Rico is joining US as 51st state and per your "popular sovereignty" doctrine wants to keep their criminal abortion statute that prohibits abortion for reasons other than protecting the woman’s life. That is clearly in conflict with Roe v Wade, but hey, it's their decision to make. Right? No, you lefties would beat them into submission to drop the statute before they get admitted to the Union.
So you adjusted your analogy to a better one and then undermined it with a speculation fallacy.
But just for the sake of describing what "popular sovereignty" means, which does not permit your conclusion leap, yes it could work that way. Given Roe v. Wade is the law of the land, the hypothetical PR law would have to go bye-bye as a condition of statehood, so if a "popular sovereignty" were in effect, PR could choose to keep its law, as could any other entering state. And that's a "states rights", small government position.
Any version of such a "popular sovereignty" does not, and can not, presume what the various states' individual decisions would be. There's no sure way to tell if a future Montana or a future Arizona was going to be sympathetic to Slavery or not, but given the trends of the time, with the peculiar institution going down all over the Americas and under fire from within the US, the pro-Slavery section (the South) saw its influence likely
dwindling as those new states came in,,
which is both why they rejected Douglas AND why they seceded to form their own country where they
wouldn't lose that influence. For that matter it's why they also kicked the Democratic Party convention out of Charleston in 1860 because "popular sovereignty" just wasn't going to go far enough for their ambitions.
In other words "popular sovereignty" was a crapshoot, and the South didn't like their odds in it.