This is definitely a hard one. It seems like in past years they did transfers during the year so if you were selected by an earlier board and then didn't get into your #1 school, you still had plenty of time to transfer it. This year they are pretty much just now actually starting to approve transfers which makes it very frustrating if you are waiting and needing to make decisions, deposits, etc!
One thing to consider is if your reach is a popular NROTC school, or one that's a reach for nearly everyone. Many people would consider Notre Dame as a reach school, but it's also extremely popular for NROTC. If you don't have it as #1, there's probably a low chance of later getting your scholarship changed there. However, if your reach is Northwestern, they tend to not fill all of their slots so even though it's a reach for you, you could probably safely list it lower and then transfer if you did manage to get in. Maybe. Of course all this changes year to year and minute to minute it seems like!
I'll tell you our experience and let you draw your own conclusions - I just asked my son your question and he said honestly he wouldn't know what to recommend to someone else. His #1 was MIT (definitely a reach) and #2 was Michigan (not totally a reach, but out of state so a bit tougher). He listed them in that order, just figuring that MIT would be harder to get into but we didn't know that the MIT unit pretty much never fills (because the school IS so hard to get into). So come November he got the NROTC scholarship assigned to MIT, then in Dec. got accepted to Michigan but deferred by MIT.
Asked immediately to transfer the scholarship and was told that he had to be on the waitlist and that pretty much anyone from a future board (and there were a zillion more of them it seemed like) had priority on getting assigned to Michigan ahead of him. For those 3 months or so I felt stupid that I hadn't researched all this beforehand and told him to put Michigan as #1 so at least he'd have one sure thing!
But in the meantime the MIT NROTC folks were in contact with him a lot. The various mids emailed him, he talked to the commander on the phone, along with a couple of the other officers, etc. Which I don't think they would have had he not had the scholarship assigned there. And come mid-March, he was accepted to MIT! I honestly feel that it was that last "kick" by the ROTC folks that pushed the application over the line from deferred (and eventually rejected) to accepted! And of course he's thrilled. But basically I feel like we took a huge gamble and luckily it paid off but a lot of people wouldn't be so lucky (and I really feel with a lot of the reach schools it comes down to luck).
Best of luck to you - you could probably start researching now and asking the units you're interested in if they do normally fill and try to make a reasonable decision from there but I'm still not sure I would have done what we did had we had all the facts in the first place!