Sure, that's what people mean when they say "if you want to House Rule it in your saga, you can do so."
But I would note that Loki isn't human, but a frost giant. So his essential nature would be different than that of a human. Comparing a human maga with Loki is the same as comparing a human maga with a mountain. Completely different essential natures.
okay, first Loki is half frost Giant half Norse god- which means either magical or faerie and what faeries can do isn't limited by essential nature
on to the main discussion:
Loki is a Jotnar, not a frost giant. He is not a giant in the sense that he is not particularly big nor are his jotnar kin. He is not frost in the sense that he has no particular affinity for frost cold or ice. The old norse word Jotnar is a cognate to the english word "ettin" and ettin is much better descriptor than frost giant. (this is the same family of creatures as grendel from beowulf, the root of name jotnar/ettin is a proto-germanic word meaning "to eat" so the jotnar/ettin could perhaps even just be rendered as "the eaters", although they dont seem to universally have an association with eating in norse or old english mythologies.)
On the topic of using muto magic to have children as a member of the opposite sex I see no reason to ban it. Muto is capable of (temporarily) overruling pretty much any other aspect of essential nature so from my point of view there is no reason to exclude fertility from the list of allowed transformations. The core book gives the example of a fat one armed man being transformed into a wolf becoming a fat 3 legged male wolf. I read this to say that anything not specifically changed by the Muto spell remains as it was. In the context of that example I think that the implied interpretation is that a fertile woman transformed into a man becomes a fertile man unless the spell specifically works otherwise. The fertility of the person is unchanged by the Muto spell.
Given that Silveroak has kindly informed us that affecting fertility is currently outside of hermetic magic I think it is fair to conclude that a Muto spell that specifically changes a persons fertility for the duration of the spell is not possible without a breakthrough.
This should be even simpler in the direction proposed by the OP (female maga becomes male to impregnate a female). Even in medieval times people would have known that a man is only briefly necessary to ensure pregnancy so Aristotelian philosophy must have an allowance for that in its explanation of human reproductive biology.
There is also the meta perspective to consider. Are you creating interesting stories (interesting as in: stories you want to play) by allowing magi to bear children as whatever sex they prefer. If the answer is yes then in my eyes the RAW is absolutely open for that interpretation. If the answer is no, then that is also allowable by RAW (but in my opinion less well supported).
The dyed in the wool medieval Aristotelian scholar would likely first blow his nose because of the vulgarity of that argument, and then perhaps explain, how the yeast added to the mash is the cause of the beer. 
Vulgar or not, said aristotelian scholar would perhaps not claim that we need to continually add yeast to the mash in order to get beer? We add it once and it does its own thing and we get a finished product. Similarly the "yeast" of the man can be added to the mash of the womb and result in a beerby (beer baby)?
I am not trying to overturn the statement that the child is actually present in the spermae and that the woman is simply "cooking" the baby. Merely claiming that said cooking can be done without the continual presence or even existence of the man.
AFAICS the Aristotelian wouldn't object to that. 
Aristotle explicitly claimed that humans were engendered by homonucleae (nucleus of man) which were found in semen and grew in women as seeds grew in the earth. So in aristotelean philosophy, male fertility produced seeds while female fertility allowed them to grow without contributing to what they were, potentially influencing development and not allowing some things to grow- then again greek mythology was filled with stories of women becoming pregnant by animals so even that limiting ability might not have been present... interestingly though in such stories the result was a deformed human (minotaur for example) rather than something essentially an animal, so perhaps the greeks simply disregarded Aristotle's philosophy on the subject...
Rather, Greek mythology was just disregarded by Aristotle. Look up the timeline!
Aristotle also cannot account for why children often resemble both their fathers and their mothers, something that is obvious to any person who has every seen any family, which means that IMO it can safely be assumed to be true and common knowledge in ArM that mothers do contribute to their children.
Lastly I at least have grown up with fairy tales that involve women becoming men and having children as well as stories of non-human beings shapeshifting to men and impregnating women. Which to me implies that the phenomenon is not considered completely unthinkable in folklore.
Aristotle isn't that dumb.
Wish to hit the libraries and look this up: Journal of the History of Biology 39 (2006): Devin Henry: Aristotle on the Mechanism of Inheritance?
I would love to, but unfortunately there is a paywall. 
This will give you a good summary:
I understand.
Stanford Encyclopedia of Philosophy: Aristotle's Biology is free, but less to the point. It summarizes: " In the closing chapters of book I (scilicet: of On the Generation of Animals), Aristotle argues that both the male and female contributions are formed from a ‘useful residue’ of blood by a concocting process, the male’s being more fully concocted than the female’s."