that might be true, and as someone who enjoys harem, I'm gratefull, but It was never the objective of this, the story is more concieved as a monogamous one with only Maria as your significant other, but yeah given how Pandaman handled this the outcome what you describe is withing the posibilitys.
Technically, if you're on the throuple or harem route it's no longer monogamous but more of a hierarchal polyamory. At present, Maria is definitely the primary partner and Emilia a secondary partner, with Luna and Zaya potentially becoming tertiary partners. It seems like the agreement between Maria and Emilia isn't likely to result in them becoming truly equitable in the short term (if ever), but the relationship is so new that it's hard to predict what the structure might look like 1, 5, 10, or more years from now as the newer bonds strengthen and they raise children together.
This is especially true given how much more sexually open the Remnants appear to be. The MC, Maria, and Emilia are still somewhat shaking off their old beliefs and might become increasingly open to new ideas as they spend more and more time interacting with their society. I'm not saying I expect polyamorous marriage to become common necessarily, but since they're essentially establishing a new society that includes people with rather progressive views, the opportunity is there.