The 12V Li-Ions are 4 packs of 3.2V LiFePO4 cells which are considerably bigger for the same charge capacity. They have lower energy density than the LiPos. There's no reason to use a 12V pack when you can use a single LiPo cell for boost or a dual cell LiPo pack for buck. People usually use the 12V Li-Ions to replace lead-acid batteries. They're popular for motorcycles because they offer some weight savings.
It's possible to get LiPos with built-in protection circuitry, but not with higher discharge rates (or C ratings). Most of the protected LiPos are 2C so if you used a 1000mAh cell, for example, you'd only be able to get 2A out of it. Though, you could probably get by with a couple protected LiPos using a buck regulator. The ones with the higher rates needed for boost are typically not available with protection. It's pretty much the same situation as protected round cells versus IMR round cells.
The LiPos for RC model applications are the best fit for the lowest cost, though the C rating is at least double what's needed. Energy density is traded off for higher drain so, if possible, it's better to use only the required C rating.
LiPos have limited availability in small quantities. There's nothing inexpensive that I've found around 10C which would be the ideal drain rate (like an IMR round cell). BatterySpace sells 10C LiPo cells individually, but they're pricey. Single LiPo cells and 2S LiPos are available from HobbyKing for cheap, but they're 20C minimum. If I could find a 10C cell around 2500mAh for cheap, I'd have the the perfect cell for a booster. I'm using the 20C 2200mAh individual cells from HobbyKing right now. I'm always on the lookout for a cheap 10C LiPo, but that's a rare bird.