Re: Samurai, Bosses are typically immune to effects like Iai Strike in FF so it wouldn't be an unreasonable houserule to say that Bosses and End-Bosses are immune.
As for Fighter's Omnistrike... Yeah, I've got nothing. What's the difference in properties between "making an attack with a weapon" and "having the weapon equipped"? You obviously get the benefits of Martial Flexibility on every weapon (since they're all equipped), but do you get the tags? The damage? The range?