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3.5 got rid of handedness. In 3.0, if you were right handed, and you did anything with your left hand, you got penalized -4 on it unless you had the Ambidextarity feat. Monks had an explicit work around for this, stating that a monk can strike unarmed with either limb, or any part of their body without suffering offhand penalties. Basically, monks were given a half version of Ambidextarity that only applies to striking unarmed.
Fast forward a half an edition. 3.5 eliminated handedness. Everyone is able to attack with whatever hand they want, or indeed attack without hands at all. If you have, for example, a BAB of +6, and are currently wielding a longsword in your right, a shortsword in your left, and you have armor spikes, you can strike longsword/shortsword, shortsword/longsword, longsword/longsword, shortsword/shortsword, longsword/spikes, shortsword/spikes, or spikes/spikes. Order doesn't matter, as long as the highest bonus attack is first. All attacks are mainhand, since the character is only making their normal iterative attacks. Heck, he could even attack once with his longsword, drop it and the shortsword, Quickdraw a shortbow and fire that. No handedness means that all iterative attacks are mainhand, no matter which hand, if any, is used to make it. This is supported by RAW and the FAQ.
So when does a person use TWFing? TWFing is a special combat maneuver. It requires a full attack, which generally means a full round action. TWFing grants an extra attack, with some very special stipulations. First, the extra attack can't be made with any weapon used in the primary array of attacks. In the above example, if the character attacks with longsword/shortsword as primary attacks, his armor spikes would be his offhand. If he attacked longsword/longsword as his primary attacks, he could use either the shortsword or the spikes as his offhand attack. Secondly, the mechanical modifiers. Depending on your feats and the size of your offhand, this could be as much as -10 or as little as -2. Also, any attack designated as offhand receives only half +Str to damage, regardless of how it is wielded. If i TWF with a greatsword and armor spikes, my greatsword gets +1.5x Str if I use it as my primary (which means my spikes get +0.5 Str). If I make my spikes my primary, they would get normal +1x Str, while my greatsword would only get +0.5 Str, despite that it is 2handed. I'd also take major penalties since my offhand is not light.
So, how does this interact with Monks? Well, FoB is very similar to TWFing, but also different. FoB does give an extra attack, but it doesn't make that extra attack an offhand. In that way, FoB is more like Rapid Shot than TWFing. Rapid Shot gives an extra attack per round, but does not make the attacks offhanded. So, when the rules state "there is no such thing as an offhand attack for a monk fighting unarmed" that conforms with the normal rules for everyone else. The monk using just FoBs doesn't have an offhand. NOBODY in that situation has an offhand, because nobody making their normal iterative attacks has an offhand, because handedness was removed in 3.5. The only people who DO have an offhand are the people who take a full attack action which includes the TWFing combat action.
FoB, TWFing, and Rapid Shot can actually all be combined. If a Monk had the relevant feats and say, a BAB of +6, he could throw 2 shurikens with his iteratives, 1 with his FoB, 1 with his Rapid Shot, and up to 2 as offhand attacks. All penalties would be cumulative. All throws would get full +Str to damage except for the 2 made as offhand attacks, which would only get half.
The only place where there is any ambiguity is is how to treat UASs. Is it one weapon that is comprised of every striking surface of your body, as is alluded to in the combat chapter? Can a character wield more than one UAS, so to speak, as indicated by the Kensai PrC? That is grey, and relatively unclear. If it is one weapon, then it can't be combined with itself at all in TWFing, since your offhand has to be different from all of the weapons you make your primaries with. If you can wield multiple, so to speak, then you most definitely can TWF with your UAS, and you could indeed attack with FoB and TWFing in the same full attack with just your UAS. You simply separate the attacks out. Mainhand and flurry attacks deal full +Str damage. TWFing UAS attacks only get 1/2 +Str.
I hope this helps clear things up. I've done a lot of research and thinking about this topic, and I'm pretty sure I got everything right.