I haven't done a super deep dive on the impact of methods in the game yet, but it looks like most of the mechanism so far is flavor - the main checks are made to see whether or not she's fertile at all rather than whether she's using a specific form of birth control. However, seeing as there are wildly different durations for different methods I would not be surprised if some of the more "off-grid" sections of the story reduced the effectiveness of some methods.
I would assume that it matters, once you chose condoms or nothing at all and end up having intercourse, with or without consent. In such a case it would matter quite a bit and I wouldn't be shocked to see such scenes in the game at some point.
I have to admit that I also had to google what some of these options were, because while I am vaguely familiar with the concept, that is about it. I think this is another example of where the devs could utilize the tooltip function that already exists within the game. Then again, does it even matter?
There are only two ways that could go, either the devs are lying to themselves and every choice boils down to the same storyline with minor changes (in which case why make us choose in the first place?)
Even if that were the case, what would be so bad about it? I can see why someone would be overwhelmed by all the options, but I do love it, even though it is unclear what some of them do. Could the game give you a bit more feedback on that? Yes. I have said so myself, but I certainly don't mind, if some of those options only end up altering a description of a minor scene, rather that giving you an entirely different scene. If you want to play a character in a certain way, it is these minor details that make a difference.