Hmm, good question!

I'd guess some flavor intensity would be lost when you boil them,
but I don't know how it affects their sugar content, etc, and how that would affect the fermentation process.

I've made the NT pickled beets recipe. The main reason to roast the beets and to roast them the full time is it concentrates the juice and makes the beets nice and soft. When the roasted beets are cut and added to the brine, the juice rehydrates, and it makes a nice beet yogurt with the juice and brine. On another batch, I tried roasting them for a shorter time, and I got firm, less smooth beets, and the juice/brine didn't yogurt up. I would also use whey to jump start the fermentation, because the first batch when I didn't, the beets developed a thin pink mold on top. I ate the beets after scraping off the mold, and they were quite tasty, but they did have a slight slight acetone flavor on the top near the mold. My later pickled beets, I used whey, and they didn't mold.

I think boiling the beets will dilute the juice, so the brine will not yogurt up. Boiling may also leave the beets less flavorful then roasting does. They will probably work well enough, but I would recommend roasting them in future. My well roasted beet batches have turned out the best.