Because it's not really between you and them as individuals.
In the harem path, they're a pair, the same way you and Maria are a pair, and how the two of you and Emilia are a throuple - unlike the traditional harem setup, where the MC is the No. 1 of every girl, you're just the No 1 of Maria and Emilia, and they're each others No 1, and the 3+2 of you form something enjoyable for all of you - it's an extension of their relationship (et vice versa).
I haven't played the non-harem paths, but my intuition would be:
- If they get together, but you don't support them fully, they'd probably less inclined to link up, obviously.
- If they don't get together, they're probably still more concerned with each other than wanting to join an existing couple/throuple who're clearly and intensely in love with each other - remember, you're not doing the usual "I'm the MC recruiting members for my harem" thing.