Is every girl MC is getting with actually one of his daughters?
We have no reason to believe, or even suspect, this for the 1999 LIs. For the 2019 LIs, as yet, it isn't possible--MC hasn't had sex with anyone at an appropriate time to have fathered any of the 2019 LIs. Skylar is the right age, but Cindy cock-blocked him and seems to have scared Luna off; Tiffany's already pregnant with Jessica; everyone else in 2019 is too young for MC to have fathered them in 1999. Of course, story developments yet to happen could change that, but it isn't possible with what we've seen so far.
I had been convinced that Skylar was MC's daughter, because I was sure he would get it on with 1999 Luna--and things were definitely heading that way when Cindy did her thing. It's possible that MC could come back to (or "stay in;" he hasn't left yet) 1999 and they get back together, but that isn't the vibe I'm getting. And "MC is actually Skylar's father" would pretty well explain her reaction on seeing him again in 2019, but how that comes to be the case given the circumstances of their parting is unclear at best. I'm now leaning toward "Luna thinks MC is dead" as that explanation, aside from the obvious shock of seeing him look identical to when she saw him 20 years ago, without his having aged a day (and actually a little younger, though not perceptibly so).
And Patreon rules being what they apparently are, at best, it'd be vague. For example, if MC and Luna had sex before Cindy came in, that makes it possible that MC is Skylar's father. If nothing further is said on the question, it'd be up to the player to decide whether that's the case or not. But it would never be said.
As to pregnancies at all, we have the option to finish inside in most of the sex scenes, and in many of those, doing so sets a variable for the game. Whether that will result in future pregnancies (or past pregnancies, in the case of the 1999 LIs) is anybody's guess, but I'd guess it's likely. But probably, as Meiri says, as an epilogue.