[dkmuldoon]

I have it turned on, but the problem mentioned by the OP doesn't seem to be fixed yet. As far as I can see on my character, as described by the OP, the boost doesn't seem to stack if you've already spent a normal boost to mitigate your normal ancestral penalty in that stat, even though that is explicitly allowed by the rule.

For instance, I've made an Iruxi witch, and I want him to start at 18 intelligence. I get normal bumps to INT from 1st level, ancestry, class, and background, however because Iruxi have an ancestral penalty to INT, that only gets me to 16. I choose to take voluntary flaws to STR and CHA to get an extra bump to INT to get back up to 18 (something that is explicitly allowed by the sidebar in the book, even though I already have an ancestral bump to INT). HLO, however, doesn't seem to allow the normal ancestral bump and the voluntary flaw bump to both apply, so only shows a 16.