I've read the following passage and I wonder if it really implies what it seems to imply.
The gravity of the offence is determined by the degree of lust
motivating the action and the qualities of the person against whom
the transgression is committed.
When the lust is very strong, even incest and rape can be committed, the most serious being the rape of a female Arahant.
If it does, why is raping a non-arahant less serious? After all, the lust is equally harmful in both cases, but in the non-arahant scenario the rape is additionally harmful to the psyche of the victim, which wouldn't be the case for an arahant. So why the act that has more negative consequences is considered less serious? And why are men and women treated unequally in this regard?
The passage doesn't imply that at all. It's just that homosexual misbehavior or other abnormal ways of breaking the 3rd precept are not discussed here.
Gravity of the offence also depends on the purity of the being who's subjected to it. Not on how he/she deals with it. It's similar to how merits of giving dependent on the virtuousness of the recipient. Not on how much he/she craves for what is given.
This sort of an offence doesn't have any difference on gender but the act itself.An arahant is a person who is higher than the everyday person because that person who we as Buddhists consider holy has reached nirvana and therefore contains no anger (Patigha),Temptations (Thanha),Confusion (Viyapada).Because of this reason they are equally great and gender plays no role in this (Being Male or Female doesn't matter),So the offence is equal among genders.But there is a difference,If you take someone who is not arahant the offence becomes different.Why?Because a non arahant monk (again being Male or Female doesn't matter!)is less great compared to an arahant,therefore the Bad karma generated by it would still be very bad but less powerful compared to what would happen with an arahant. Please note that unlike religions like Christianity,Buddhism pays no attention to a persons sexual attraction so this Homosexual or being straight notion doesn't matter at all.Mainly because Karma doesn't recognize gender as an variable it is only a natural mechanism of you actions causing consequences.All the circumstances mentioned above in your question causes extremely lethal karma and most likely a person committing such an act would not see another day (In reference to a story mention about a female arahant being raped by a young man).