Since your post sounds as though you plan to be careful then you're probably aware there are risks to using Li-Ion cells. It's the type in news reports of rechargeable batteries causing fires and explosions.
Your data sheet link mentions their testing methods did not cause fire or explosion. However it makes one wonder whether they did experiments that DID cause fire or explosion! Reading between the lines I sense the data sheet giving us implied warnings about using Li-Ion cells.
I remember the first rechargeables on the consumer market were types able to tolerate a certain amount of abuse. Nicad, then NIMH. Evidently the push to miniaturization has encouraged manufacturers to give us a type that requires extra care (Li-ion). I'm not a Li-ion expert though I guess your description of your circuitry seems to include extra care.