If they're non protected, it's possible that the nature of flashlight use (forgotten and just left on somewhere) could drain them beyond their lower voltage limit, and after that they tend to get explodey when you try to recharge them in a dumb charger.
Also, LiOn RCR123's charge up to 4.6V peak, which in a two cell flashlight is 9.2V, when it may have only been expecting 6V from 123a lithium primaries. Some incandescent bulbs can't handle it, or in the case of LED's the driver/regulator can't.
It's just a CYA thing on their part. It's up to you to read/get the exact specifications of whatever it is you intend to use them in.
RCR123a's are 4.2v max. Not 4.6v. All Li-Ion technology batteries are natively 4.2v max with 3.6v nominal. Some just have protection circuits that drop it down to 3.4v max I think and 3v nominal, so they can be used in devices that 4.2v (or 8.4v when using two) would kill.