Glad you asked!
The first thing is to recognize that the Vinaya itself doesn’t explain these points, so any explanation is hypothetical.
The second thing is that there is only a very loose relation between the severity of an offence in Vinaya terms and the actual moral gravity of an act.
Here’s some extreme examples. Suppose I, as a bhikkhu, wander into a bookstore. I see a nicely bound edition of, oh, I don’t know, some random book, say, Animal Farm. I think, “Wow, that looks nice; it would be wonderful to read a playful fairy tale with no parallels to our current political climate. But I can’t buy it.” So I glance around the store, and, thinking to steal it, pick it up. But as soon as I have it in my hands, I come to my senses. I realize what I’m doing and put it back. Still, I have committed a parajika: I am not a monk, and can never be one for the rest of my life.
On the other hand, suppose that I enjoy bashing homeless people. At night, as a monk, I go out dressed as Neo from the Matrix, and beat up helpless people on the streets. I do this because I don’t like the way homeless people bring down the tone of my recently gentrified neighborhood.* Doing this, I incur multiple pacittiya offences, which I can clear by simply confessing at the next patimokkha.
Okay, that is, like I said, an extreme example, but you get my point.
So when considering the rules regarding masturbation for monks and nuns, the moral gravity of the acts have a very loose relation to the class of Vinaya offence.
What other considerations are at work? Well, one of the basic considerations for Vinaya, as with any legal system, is simplicity and knowability. Consider driving, for example. If there is a law saying you can’t drive over 60kph in this zone, this is clear and straightforward and easy to enforce. But there are many silly things you can do in a car without going over the speed limit. So, to cover cases not explicitly mentioned elsewhere, they make a law against “dangerous driving”. But this is highly subjective, and much harder to pin down. That doesn’t mean it can’t be done, it just means it’s not so simple.
I think the same thing is at work here. Note that the monks’ sanghadisesa occurs only at the time of ejaculation. Anything else is a lesser offence. This makes sense, as it is hard to define clear cut boundaries in the various stages of arousal and stimulation. Female sexual response is less obvious, and it is harder to define in a clear cut way, especially from an external point of view. I am not even sure whether there was a clear understanding of the female orgasm at all. In fact, if there was not, this alone would be a sufficient explanation.
We should also bear in mind the question of authorship. We don’t really know who authored these rules. In Bhikkhuni Vinaya Studies I have shown that there is, in some cases, a specific set of terms that suggests the nuns had an independent code. But whether these specific rules were authored by the Buddha, by the monks, or by the nuns, is unclear. Obviously if there were male authors, we could expect less understanding of such issues; this could even be used as a principle to evaluate authorship.
Yeah, no, I don’t think so. The Vinaya is relentlessly rational, and ignores such magical thinking even in cases where you would clearly expect it, such as the treatment of menstruation.
* Based on a true story: it happened in Wolloomolloo. Not a monk, though!