Even today, a large majority of women are attracted to grotesque men for inexplicable reasons. Why is rape the first explanation on your mind? Lol

If only based on typical human behaviour: Probably both. There’s always someone that’s into something a bit different, so if Sapiens and Neaderthals intermixed sufficiently, there’ll always be some couple that gets it on. Hell, there’s people that fuck dogs (and dogs that try to fuck people). If dogs had been capable of consenting, I’m absolutely positive that some consenting human/dog couple would exist. I would say that consenting inter-species couples would have been inevitable given enough mixing of the groups.

Then there’s also the long history of sexual violence in conflicts. Sapiens and Neanderthals were competing for resources, so there’s bound to have been tribal conflict at some point. Just based on how humans behave in that kind of situation, it’s pretty much guaranteed that people were raped during those conflicts.