Li-ion battery life after being 'completely' discharged
If the voltage of a lithium-ion cell drops below a certain level, it's ruined.

That statement is a bit short sighted, it depends on the actual type/brand/model/chemistry (there are several Lithium based types) if this is true. According to tests by BigClive (sorry, I cannot recall exactly in which video he mentions this) some batteries can be completely discharged (0 Volts), charged again and then appear to still have their full capacity. Note that the "fully discharged" state did not last long (hours or days perhaps).

Lithium-ion batteries age

That is true but also depends everything I mention above and also how you treat the battery. For example in some military applications Li-Ion cells are charged not up to 4.1 - 4.2 V (like in many consumer products) but to 3.8 V or less. This places less stress in the cells making them last longer.

but I assume Apple doesn't charge the devices to 100% anyway

That will actually be the battery manufacturer producing the batteries in such a way that they are at around 40% to 60% charge when finished. They're not charged or discharged as that takes too long! The charge level can be set by using the proper ratios of chemicals during production. Same as non rechargeable batteries are made to have 100% charge.

If you want to store a device for some time, I suggest charging the battery to a value between 40% to 70 % (my rough estimate). Then if possible remove the battery! 

If removing the battery is not possible make sure that the device is switched off and store it in a location where it cannot get very hot or cold.

To protect against fire and overcharging (when the charging circuit in a product breaks) nearly any device will have a battery protection circuit. This will simply disconnect the battery when the battery is in danger. I am quite sure Apple devices have this.

BTW, this does not protect against manufacturing issues with batteries which is often the cause of batteries catching fire.