Some cells are a bit larger than others, but that's more to do with loose manufacturing tolerances.
Also, from the
Welcome Mat:
Q: What do protected/unprotected mean in regards to Lithium-Ion?
A: As mentioned in the "what is double-tapping" question, a "protected" Li-Ion has a small electronic circuit integrated into the cell packaging. It protects against common dangers, such as overcharge, overdischarge, short-circuit (overcurrent), and temperature. These cells are safer to use, both individually and in batteries. They are less likely to ignite and cause personal or property damage, a phenomenon known as "venting with flame." Unprotected cells do not have this protection circuit, so they can have more capacity and current capability than protected cells. Some cells, such as 10440 (AAA), are too small to accomodate a protection circuit and are only available in unprotected form. Users must decide whether they prefer to stick with protected cells or accept the bigger responsibility and danger associated with unprotected cells.