Conclusions: in the case of Alexander, the boss weapons copied are more commonly different projectile configuration data for weapons which he already has (minus the boss form of Julien, which is just a base melee upgrade).
In the cases of Julien and Michael the boss weapons are actual *weapons* presumably reverse-engineered to exhibit some degree of power similar to that of any given boss (minus the boss form of Alexander, which is just a base ranged upgrade)
Helena is a lot more like Zero in that most of her weapons are really just extra special moves, only one or two of which actually has ‘weapon energy’.
Miles is another large division of his own, in that his adorable baby Codex of the Infinite Planes prefers to take a sample of boss energy and turn it into a flat-out support summon. He’s… weird. For the intro levels he’s pretty much a joke though, considering his main attack is a knife with a range of about seven pixels.