Throw Anything and Catch off guard are weird feats.
They are basically Weapon Proficiency (Improvised).
Clearly, they are not meant to replace individual weapon proficiency feats - that would make them too good. So we have to say, 'no, a longsword is real weapon - you can't use Catch Off-guard with it.'
But that leads to the weird situation where an Alchemist (since they all get Throw Anything to go with their bombs) is better at throwing a beer stein or a rock than a throwing axe, which is meant to be thrown. (Your GM might decide the rock only does 1d4 damage, but 1d4 that hits is better than 1d6 that doesn't.)
Arguably, he's equally good at throwing a throwing axe (it is part of the superset "everything"). But if he does, he throws it like a weighty stick and it does a d4 when it hits (and it probably doesn't hit with its sharp edge).
Now, if he wants to throw the throwing axe properly, so that it strikes sharp-edge first and causes maximum damage, he should look at becoming proficient with it.
It gets weirder with spears. Someone not proficient with a spear could get throw anything and, presumably throw it backwards or something else equally ridiculous, to do his 1d4 "anything" damage - I guess he's not proficient enough to figure out that the pointy end is more effective...
