It really depends on what your desired outcome is.
If you want a nice white, purer end result, do the 3 boils, decant from the plant matter, base and pull with naptha/heptane.
If you want a nice orange, full spectrum spice, then you can do the a/b with the plant matter still in the mother liquid and pull with warm naptha or room temp xylene. Check out the BLAB on the wiki for more info.
Your yields will typically be a little better using a BLAB with xylene or d-limo because they tend to pull a bit more fats and oils out with the spice. You can still get good yields with a regular A/B, it will just be a lot cleaner.
As far as unwanted compounds go... The way I see it, these plants have evolved to produce these alkaloids and compounds for us to use. I figure they are put there for a reason, so why not take advantage of them?
So when you ask which you should do, I say do both so you can figure out which result you enjoy more.
Convert a melodic element into a rhythmic element...