You might be sacrificing ease of adjustability doing that, but I can't see how it would be unsafe, especially since half breeds are used on the off side when you want to make sure it is all extra secure. You're looping double thickness of leather twice plus utilizing the cinch buckle -- makes it no different than double looping then using the buckle on the cinch instead of tying the latigo.
Well, depending on the hole placement, you might have to make compromises in how tight you get the cinch when you adjust/take up the cinch. If you have to crank on it a little hard to get to the next hole, you will very likely create a cinchy horse. Not good, and not safe (when the horse blows up and you think the cinch is tight, but it isn't). If you settle for the lower hole, that is too loose, you won't get the horse cinchy but the cinch won't be tight enough to get on.
If you have enough holes so that you aren't compromising the adjustment of your cinch, great- no problem.
The usual latigo gives you infinite adjustment, and most of them have holes punched so you can either use holes, or not.