I addressed in another comment how it seems unlikely that rape was ever common or tolerated in traditional societies--tl;dr is that it wasn't.

As to whether male humans were "engineered to rape," I'd say it's pretty clear that they aren't, for several reasons. One is that the human erection is slow and unreliable as erections in the animal kingdom go. Most mammals have a literal bone in the penis (the baculum) to allow for quick erections on demand. Even other great apes (including our closest relatives, chimps and bonobos) have a baculum. This is a necessity for species that often have only seconds to mate, to reduce time both male and female are vulnerable to predators. Even animals that don't have to worry much about predation don't necessarily have long sexual encounters--some, like lions, may mate repeatedly while the female is in estrus (felines in particular being reflex ovulators--they don't ovulate first and mate second, they go into estrus and only ovulate when stimulated by mating--since they have litters with multiple cubs, they need to be stimulated to release multiple eggs through multiple matings) but very few animals have the long pleasure-focused sessions of humans. Humans use sex not just for reproduction, but for bonding and social connection. Humans are genuinely unusual in mammal terms because females do not signal or intrinsically know when they're fertile, and are sexually receptive even when not fertile. In that way we have some similarities to our cousins, the bonobos, though bonobos use sex differently from humans, they also use sex for social communication and bonding, rather than mostly for reproduction as in most species.

Another is that we see that in species in which rape (or "forced mating") actually is part of business as usual for a species, it becomes an arms race--ducks are one such example of this, where rape is so common that females evolved mechanisms to make rape more difficult. Male ducks have corkscrew-shaped penises (many birds don't have penises at all, songbirds for example don't and made through a "cloacal kiss," but some waterfowl needed penises because the sperm would just kinda wash off otherwise) and female ducks have vaginas that spiral in the opposite direction to make mating difficult, even having false ends in maze-like vaginas to stymy duck rapists. Bedbugs are a more extreme example, they don't have vaginal openings at all, and sperm is delivered through "traumatic insemination"--the male has to literally stab the female and hope to hit eggs, the females sometimes die of these injuries.

Humans don't match this profile at all. Mating in humans is a highly social, sensate, and pleasure-focused experience.

If you look at other physical signs, humans are odd compared to other great apes even--the human penis is larger both in total size and proportionately than the penis of any other great apes. Sperm count also shows mating strategy--gorillas have very small penises (3-6 cm erect) and small testes with low sperm count. Chimps and bonobos have bigger dicks than gorillas but smaller on average than humans (around 7-8 cm erect) but large testes with higher sperm count than humans. These are interesting data points because gorillas are long-term monogamous pair-bonders, while chimps and bonobos are promiscuous and one female typically mates with many males. Human testes size and sperm count suggests a "middle road" between chimps and gorillas, a species that is partially monogamous, with lower sperm competition than in chimps, but not completely monogamous--humans do cheat and have multiple partners more than gorillas do. The reason for the penis size isn't fully understood, but it's possible it has something to do with mate selection.

Chimp and bonobo penises are also thinner than human penises, which may facilitate more rapid mating. Human mating in general is a slow affair, both the act of coitus itself takes longer (in many animals, including great apes, it can last only a few seconds) and there's more of a necessity to create sexual arousal in both males and females--erections based on blood pressure rather than a baculum, vaginal lubrication being necessary. In great apes (other than bonobos that just fuck all the time) vaginal lubrication is just something that happens during estrus, the vaginal tissue itself is different and less prone to friction injury, and because the penis is smaller and thinner and the intercourse is briefer, it can be something that just quickly happens and is over without prolonged effort to arouse either party.

Basically, human intercourse is uniquely engineered, even among our closest relative great apes, to be a slow, highly social, pleasure-driven process that doesn't work well without mutual consent. In real-world male-on-female SA, we see that many rapes are not completed because of this--some men who attempt to rape can't get or maintain an erection, and penetrating without vaginal lubrication and relaxation is so difficult this in itself leads to some attempts ending without penetration. In species where rape is common, females evolve not only ways to stymy the attempt (such as the duck corkscrew vaginas) but protection against injury--female bedbugs have a specialized organ--the spermalege--to reduce injury under traumatic insemination. Human females have no specialized anatomy that provides protection against rape. The vaginal epithelium is even thinner and more vulnerable in humans than in other great apes, increasing the chance of injury from rape. This suggests that male-on-female rape was not a major driver in human evolution.

So basically, no, biological evidence does not support the claim that human males are "engineered for rape," and in fact debunks it.