Good question!

Sodium ion already had a reduced capacity (30% less at least than Lithium ion). And 2.5% of voltage is not 2.5% of capacity, something more like 3-4% (still small)

You could then just choose to use a configurable lithium ion IC, but almost all of those have an undervoltage lock out (safety shutoff) that is 2-2.5V that you would have to stay above. Sodium ion drops out at 1.5V, so I would again be losing a chunk of capacity. If I lost 30%-35% of capacity on an already reduced capacity cell compared to lithium ion, then battery life would be quite disappointing.

Do that rules out using a standard Lithium-ion charger.

If I am building a custom charger anyway (most non- embedded systems have custom chargers), then might as well put in all the features now and get 100% of the capacity. Cells usually also have a higher lifespan (double or more) by dropping that high CV charge voltage 0.1V or so and settling for lower capacity, but Sodium Ion lifespan is already 3000-5000 cycles compares to lithium's 500-1000 (lithium ion and li-po, lithium iron phosphate is in the higher range) so might as well then use the full capacity.

They don't. Outside of the lab, they just recalibrate and call 95% "100".

Some people who are like "I bought 100% of my product so I shall use 100%"