Some spots will be gone right away, but some programs wait until after the MD match to fill their spots because they want to scoop up candidates who didn't match in the MD match. Some programs actually expect scramble candidates to travel to the program for an interview!
As for the choice of whether to rank less than ideal programs vs. scrambling (I realize that for the DO match this year this is academic but I am adding this for the benefit of people still making lists for the MD match and in the future), as someone who has been through the scramble, I really do recommend ranking everywhere you interviewed unless there was something very seriously wrong with the program.
If the program's culture seemed extremely malignant and you're worried you would have to drop out of the residency rather than being able to tolerate finishing there, yes, that may be a good reason not to rank it! However, if the reason is something like (for example) you really like living in California and you don't want to rank this program because it's in Flint MI and you're hoping maybe you can scramble into a program in a nicer location, then that's a very bad idea.
At least with programs you applied to and interviewed at, it's "the devil you know" and if you applied to the program that probably means *something* attracted you there in the first place.
The scramble is much less predictable. Think about it: Why is the program in the scramble? Usually, it's because something turned off applicants to the program enough not to rank it. Perhaps the reason the program ended up in the scramble is something that isn't a big deal to you, but the scramble doesn't give you the luxury of having as much time to investigate a program and you may not even see the place in person before you choose to accept their offer, so you can't be sure you have the full story about what it's like.
The spots available in scramble are also so unpredictable. Yes, you can probably expect a lot of primary care spots to be open - but nobody really knows for sure how many spots will be available from one year to the next OR what quality they will be.
Some years, the match/scramble is worse than others. Medical school class sizes have been growing over the last few years meaning the competition for residency spots is increasing and there may not be as many open spots in the scramble as there were in previous years.
Even if a spot you do really want is available in the scramble, you will often be under pressure to decide whether to accept a spot at a place you don't like as much or risk holding out for an offer from your preferred place but then risking that you'll end up with nothing.
The reason that I ended up having to scramble is because I chose to only go through the MD match even though I had interviewed at a DO program that was pretty decent and where they seemed to like me well enough that I think I would have matched there if I had ranked it.
In my case, there was nothing particularly wrong with the DO program - I just liked some of the MD programs I interviewed at better and wanted a chance at them. However, that DO program sure started to look a lot better after I didn't match! I would have been perfectly happy there if I had known then what I know now.
I don't like to see people going through the scramble if they don't have to, simply because the process is very stressful and less than ideal. I hope that nobody reading this ends up having to scramble, but even if it does come down to scrambling, I wish you the best.

In the end, things turned out fine for me - I just would have rather not gotten to where I am "the hard way".
🙂