My sincere apologies if other people caught on to this before me and I'm really just embarrassing myself. I post only sporadically here.
In HG101's R-Type article, they dismiss one of R-Type Final's stages as people at Irem either trying to be 'daringly artful, or having strange issues'.
I'm talking about the background, displaying a couple getting it on, proceeding towards doing the nasty as the stage progresses.
Just the Japanese being Japanese, yes?
Or what if what's happening in the foreground is really just a metaphor for the process of impregnation?

It's one of those things that, once seen, can't quite ever be unseen, much like Whoopi Goldberg's lack of eyebrows.
It's not as if Irem has never explored this theme before. R-Type III, second boss? (Japanese version, not the neutered US one)
After defeating Gomander, you fly through what the article describes as an 'alien vagina', after which you try to overcome the womb's defenses to try and blast the embryonic last boss with the Wave Cannon, which could be interpreted as DNA.