So I made a couple changes, and I got it to work. The issue is, at least in my experience, that Time Machine won't work in any directory except for the user's home directory. This may come down to some kind of permissions error and that's why it worked in the home directory. I'm not 100% sure.
One "regression" I have had in terms of coming from a Synology device using Time Machine is that when I was on the Synology, I had a separate user for each Mac that I was backing up, and I could set user-level quotas on each user, such that the MacBook Pro had way more space for backups than the MacBook Air, etc.
It seems tough to do that in the current implementation. Because I can only set the quota on the dataset level, and it's only recommended to have one Time Machine AFP share per network, the way I have it set up now is that I have one "Time Machine" dataset with one "macbackup" user. The user has his home directory within the Time Machine dataset, and then all 3 Macs backup to there. This works, and I have a 2.2TB quota set on the Time Machine dataset.
I think there are two features / fixes that would make this a bit more ideal for me.
1) I'd like Time Machine to work in a directory that isn't the user's home directory. I'll play with this a little more. Maybe this is possible. When I first got this set up, I knew a lot less about FreeNAS permissions than I did by the end of last night!
2) I'd love user-level quotas. I know this is a feature that is being worked on so we'll get it eventually!
