You can do that, but they will be two separate reservations. You can ask MS to "link" them, but they cannot "combine" them under the same reservation number because they are two different memberships. If this is the route you decide to take, you have to understand that while they will try to not move you from one villa to another, the possibility of it happening does exist. If Aulani works like Disney World, you will have to check out at the end of the first reservation and check back in for the second even if you are not changing rooms. Personally, I would much rather deal with the hassle of transferring points from the comfort of my home, so that I have one reservation #, rather than deal with the complication of 2 reservation numbers while on vacation.
They will not "combine" points from two different contracts in order to avoid the "straggler points" that you are referring to. If you want to avoid orphaned points, the best way to do it would be to do a points transfer and then make the reservation in a single phone call.