Often you will not use the max for the secondary protection. For example, probably the most common transformer in the low voltage world is a 75kva 480 delta to 208y/120. This would have a secondary current of 208 amps (and a 50kva single phase with 240 secondary is the same secondary current and also super common). Most of the time the secondary conductors will feed a 200A MB panelboard. Of course you could go 225 or even 300 using the next size up allowance in note 1, but 200 is just super common and you rarely need the extra 8 amps. Remember that also the secondary protection most of the time is also meeting the requirements of 408.36 for panelboard protection and 125% of the common transformer sizes are oddball main breaker panelboard sizes.
If you had a 200 amp continuous load (or any other continuous load that is about the rating of the transformer) you would need that extra 25% for the secondary OCPD.
The primary OCPD on the other hand, many people like to size that as large as possible for inrush, but you need larger conductors to go along with it.