The first thing that came to mind when I saw the full grown aliens in the cave was where are their females? Now if it had been me writing the story there would have been a female highly pissed off that the two males were humping Earth sluts. In comes a male human with a big dick. What would she do? Of course the female would be better looking than the males but still a bit ugly. But her pheromones get our hero all hot and bothered. He proceeds to plug the most appropriate hole which the makes the aliens very mad (males are possessive) they grab the female and pull her away. She's even madder now so they get to scrapping and our hero makes off with the girls then shorts out the portal so they can't come back. When the girls heads clear from the alien influence they are highly grateful to our hero and show him just how much they appreciate him. Turns out they like being his sex slaves. So instead of them disappearing (cops and whatnot getting nosey) they continue their normal lives but when they want sex they keep it between the three of them. Maybe he and Monica have a "nooner' at work or Sako shows up in his lab for a "quicky". When they are off work the Dungeon is their playground. Anyway that's how I would have done it. Leaves less plot holes and a better flow IMHO.

I had thoughts on this subject too, and I cane to the conclusion that they could perhaps breed through parthenogenesis. As happens with reptiles, amphibians, birds, and fish. Some would change to be female if there were a surplus of males in the population.

Then why would they have a penis?

A penis would develop during the shift to male, and female sex organs would develop during the shift to female. I am basing this hypothesis on the fact that there was a little version of the creature in the cave. As for why the first one was male, well it got DNA from Peter. One possibility as to how there were two from just the initial one is cellar division.

I'd say the creatures are more like insects. Reptiles, amphibians, birds, and fish mature gradually, an insects' metamorphosis is suddenly, like the creatures's. The dormant state can be seen as a coccoon. As for why there are only male individuals, maybe they come from a male-only species that does the things we witness in TD for survival of their kind. I mean, localize and intoxicate females from other races, abduct them and use them for reproduction. And if they were male-only, that would explain their possessive behaviour, as interference from other species threaten their chances of survival. We see that they care for each other when an individual of their kind is in danger and that they show no sign of threat while fucking gnext to each other, they only do when Peter (a foreign male) comes near.

parthenogenesis also happens within insects too, 3 examples are bees, wasps, and aphids

Well, if we're going science here, lets not discount sexual dimorphism. Typically the females are the larger of the pair, so that "cave" we were running around in could be monster vag on a large creature... just sayin...

I did get the impression that the cave was somewhat representative of a creature's internal structure.

Yes, bees, wasps and some other insects have the ability of parthenogenesis.
But parthenogenesis is the ability of some females to reproduce with little to no males around in order to keep the kind alive. Their ova simply stay unfertilized or are tricked into a pseudo-fertilized state by hormonal influence and still are able to develop into full grown individuals.
Males still need female ova to reproduce. And if a species is able to somehow bypass the reproductive barrier, those males can reproduce with any female, which seems to be the case in this scenario.

Not sure if they could produce viable offspring though. The basic act of sex yeah, But the tentacle creatures are technically a different species. The point of separation being, when offspring can not be reproduced. The Original creature did get dna from Peter. There Is als9o a direct connection between Peter and the creature. Sex could still happen, without it necessarily leading to reproduction. And sex, regardless of whether it leads to reproduction or not, is a very strong base instinct. parthenogenesis still stands as one possibility as to how they reproduce among themselves. The sexual possession of Monica and Saica could be something inherited from Peter.