Jen, each plumeria should have it's own pot. Plumerias have fragile roots which break easily, but these are just starting to root so the roots won't be very long at all. It doesn't matter if some roots do break because it will continue to root. If you grab a large amount of soil around the base of the plumeria or if you carefully turn over the container and gently separate them, you should be able to separate them without disturbing the roots too much. The roots may be combined with your other plant in there so you may have to separate them.
Inflo's on rooting cuttings are not guaranteed by any means. Some people cut the inflo's off while their cutting is rooting so that energy can be directed toward rooting and not toward flowering. This is probably a wise thing to do, but that being said, I have never done it on my plumerias. I do it for all other cuttings which I'm trying to root but not for my plumerias. It is hard to do! Anyway, if the cutting does not have enough energy of its own to flower, the inflo will dry up and fall off, but the plumeria will branch at that point. Some plumerias flower and root fine at the same time. Sometimes, flowers on rooting cuttings are smaller than they would be otherwise, and sometimes the flowers are only four petals instead of five.
The answer to your question is, no, moving it will not affect the inflo, and in the long run, it is good for your plumerias to have their own space to grow in, but the inflo on a rooting cutting doesn't always bloom fully.
Here is a flower on a cutting which I am rooting now. The flower is smaller than it would be otherwise, and it only has four petals. I have other inflo's on rooting cuttings which dried up, and I have some which are starting to bloom.
