When trying decide what Throughline this is, another approach is to ask yourself if these two characters are meant to be a MC and IC pair. It's been inferred by some others but I don't think that's been overtly stated by the author.
If the answer to that question is yes, then their developing romance is the RS. If the answer is no, then their romance must be in the OS and somehow the problem element preventing them from getting together is shared by everyone in the story in some way.
That second story is probably a lot more complicated. It needs an IC to influence whoever winds up being the MC, which has the potential to crowd out the other character involved in the romance, though this could be mitigated by making that character the protagonist.
The other option, making them dual MCs, you already mentioned. In this case the characters have to have the same personal problem. They'll have to have either the same character as IC or separate ICs that are structurally the same.
Instead of looking at what you have and trying to put it into throughlines, it might be easier at this stage to look at the different directions you could go in and how each choice changes what the story will look like, so you can pick the one you prefer.
It's possible your difficulty in deciding whether the romance is RS or OS is a sign that you actually want those throughlines to share problem elements. This is a way to sort of have both, though the RS and OS will treat that element differently. This also forces the OS Outcome into Failure, which is relevant since you also mentioned this might be a personal triumph.
Can anyone of an example of a story where there was a prominent romance in the OS involving the MC, but where the MC/IC RS is something totally different?
Spider-Man 2 maybe? Assuming it's a GAS.