Opping fakeplayers is the laziest and dumbest thing you can do for your server. The plugin (or any plugin) doesn't know that JoeBlow's quarry is the quarry editing the world so it will rip right through your spawn, LWC, or anything else that is op-only. Set the fakeplayers to builder rank or whatever else you use for regular players.
In your Factions config there will be a setting for "playersWhoBypassAllProtection" That's where you would place [buildCraft] and whatever else. Again though, that means any fakeplayer can always bypass protection and I am sure you can imagine the amount of grief that you will open up by using this setting. It isn't a friendly toggle like GriefPrevention on a per-user basis: it's global. Best bet is to just tell players to quarry or whatever right outside their land.