I've been doing a bit of looking around on Torhead and came across moddable "named" companion items, eg. Kaliyo's Prototype Reinforced Blaster and Mako's Prototype Reinforced Blaster. Where are these things?

I'd guess they're quest rewards. Some quests give you a choice of reward between planet coins, item for you, or item for each of your companions. Companion weapons can be green but still modable.

Companions all start with "named" gear: Qyzen's Jacket, Kira's Boots, etc. The armor is all green and not modable, though as you advance, certain missions will give you the option for better (still green unmodable) gear for them (Qyzen's Layered Jacket, Qyzen's Field Jacket, and so on). For the most part, it's OK stuff if you haven't kept up with gearing your comp, and if it's level appropriate. But I typically have my comps geared better than those by the time they are offered, usually "blue" loot drops, and at least some modable armor.

 

They also start with a modable (but green) weapon, and/or you can choose one as a mission reward later on (Kira's Double-bladed Lightsaber, Kira's Reliable Doublesaber, etc.). But since they start with a modable weapon, I usually pass on these, and just take commendations so I can upgrade the one they already have. Though once in a while, I will take the offered item, usually because I haven't kept their gear up, so the new one is better than what I already have for them.

er than those by the time they are offered, usually "blue" loot drops, and at least some modable armor.

 

They also start with a modable (but green) weapon, and/or you can choose one as a mission reward later on (Kira's Double-bladed Lightsaber, Kira's Reliable Doublesaber, etc.). But since they start with a modable weapon, I usually pass on these, and just take commendations so I can upgrade the one they already have. Though once in a while, I will take the offered item, usually because I haven't kept their gear up, so the new one is better than what I already have for them.

 

Exception: Your first companion generally does not have a moddable weapon to start with, though any future quest weapons for them will be. Almost all other companions start with a moddable weapon, so I generally do not replace those weapons until much later on when a future reward also provides decent mod and enhancement upgrades - for the most part I just upgrade their hilts/barrels and call it good.