Putting a soul counter onto Netherborn Altar is part of the cost to activate its ability, and counting the number of soul counters is done as the ability resolves. Players may take actions between those times to change the number of soul counters, perhaps by removing them all so that you lose no life.

If Netherborn Altar leaves the battlefield while its ability is on the stack, the amount of life you lose is determined by the number of soul counters it had on it immediately before it left the battlefield.

The “commander tax” increases based on how many times a commander was cast from the command zone. Casting a commander from your hand doesn’t require that additional cost, and it doesn’t increase what the cost will be the next time you cast that commander from the command zone.

If your commander isn’t in the command zone (or if you’re not playing the Commander variant), Netherborn Altar only makes you lose life.

If you have two commanders in the command zone, Netherborn Altar’s ability puts one of your choice into your hand, not both.