because the protection can kick in , that is the main reason.
when the protection kicks in it becomes a open curcuit, so the charger wont even see the battery existing there.
and
when charging in series, and NOT using balancing, which is a dumb thing to do, one cell could be so far out of wack with the other cells, that the protection on that cell has kicked in. but that is a GOOD thing.
and depending on the protection amp rating where the short curcuit amps protection kicks in, a excessive high rate of charge from a hobby charger would kick in the protection. if the hobby charger uses a lesser charge alogrythm that doesnt do the proper charge for a li-ion, the charger will not be able to charge it fully, as it will cut out.
and depending on the protection again, there is a slight resistance change, wherin the voltage read under charge/discharge would be higher/lower than the actual voltage.
if the charger is working properly and the user isnt going crasy with the settings, and the user always balances any series pack items, the only flaws will be the protection doing what it is supposed to do. as hobby chargers can be set to do things they shouldnt do to a battery
the user in this situation with or without the protection can make all the differences in the world. the discalimers just keep them from being around when the user fails.