It is totally optional to play with mods or not in each ongoing game. The settings you put into place are also saved game/world specific. If you actually did want to use the same NRaas mod(s) and the same settings in a different ongoing game without having to set them all manually again, you could export the settings from the first game and import them into the next one. Players who always (or almost always) use the mods tend to have sets of exported settings all ready to use as that which makes sense in a crowded urban world might not so much in a sparsely populated rural one or a tropical island world. Or they might have a "minimalist" collection of settings that they use to test out new worlds they have never played before, or they prefer a different set of things happening or not happening in connected worlds within the same game like vacation destinations, Uni, and Oasis Landing.
Point is, the mod settings you put into place exist only within the saved game, within the world-specific nhd file.
The mods are also removable if you don't like them and the saved game can be played forward without them. Once a game that has seen, let's say StoryProgression, has been played and saved without the mod in place, the mod settings are erased going forward. There are a small number of things to be careful of when removing mods should this be necessary, such as yanking Traveler out when your sims are visiting a custom vacation world will result in them not being able to get back home, taking out a modded career/school while a sim is working/going to that school will leave them doing something undefined, etc. But none of these really apply to SP. If SP is removed from an ongoing save or if it's progression is disabled within its General Options, then either EA's story progression takes over or there will be no progression (to the limited extent that actually helps at all) as per the Game Options checkbox as if the mod had never been there.
Pregnancies are challenging to control when playing rotationally, but many of us see that as a welcome challenge. I take it you do not want your sims to become pregnant or impregnate others while they are not the active household. But you can allow them to be pregnant so that a pregnancy formed but that has not yet come to term when it's time to move to the next household can remain. The baby will be born when you aren't playing the household though as the pregnancy will continue to progress even if aging is off for that household unless you stall/pause the pregnancy (this is what I do) using MasterController. The MC Cheats module is required to pause pregnancies. There are other mods that can do this as well that are compatible with NRaas, such as CmarNYC's Pregnancy Controller mod from MTS. I haven't missed a birth among my many controlled households in years, and even then it was due to user error on my part -- I forgot at the time that MC Resetting the world, which I did for other reasons, removed the stalled state from one pregnancy so I just had to correct my mistake and replay a couple of sim days.