Yeah, if there's one thing I've learned from mechanical mods, it's that I don't want to over-discharge my cells. I'm guessing that your average AA cell won't fail as catastrophically as an unprotected lithium battery due to chemistry but I'd still prefer rechargeables (for most everything) to an endless stream of disposable alkaline batteries (even if I were able to squeeze a little more out of each one).
Lithium definitely isn't as resistant as alkaline to abuse, which is why consumer adoption (at least in the West) has been rather slow. Regular AAs don't catch fire or get dangerously hot when short-circuited, but that's also partly because they don't have the energy to.
Cylindrical hard-cased cells like 18650s are still safer than pouch-cell lipos though.
Deep discharge does not make LiIon cells explode (or vent), it only reduces their cycle life a bit. Though personally, I swap the batteries in mech way earlier than the point where they start getting damaged. At 3.6-3.7V the battery is weak and doesn't produce enough power on the coil. I'd be surprised if people regularly overdischarged batteries.
