Enemy ability scaling is based on two main factors: vanilla abilities and monster level. If you want to know what monster spells and abilities will be scaled into, keep reading.

First, each vanilla ability that a monster can use is placed into an Element Class. There are 11 Element Classes: Fire, Ice, Bolt, Earth, Wind, Water, Poison, Pearl, Non-elemental, Tek (Magitek), and Cure. Additionally, based on the vanilla power of the ability, a Tier Modifier is applied to the scaling.

Monsters can have access to multiple Element Classes, same as in vanilla. For example, TunnelArmr uses Bolt, Fire, Poison, and Tek Laser in vanilla. Therefore, can access abilities in the Bolt, Fire, Poison, and Tek Element Classes.

Note that for Enemy Abilities - Scale Random the Tier Modifier is still relevant, but the Element Class is randomly selected.

Next, calculate the Element Class tiers the monster can access.

but the shell counter has a +1 tier modifier so it will use stronger abilities than the head. Tiers aren't quite as simple as level x = grand train. There are 11 tiers total and tier 8 is the highest enemies reach based on their level. Generally, tier = enemy level / 5. However, to prevent trying to stop ability scaling before multiple of 5 thresholds and to create a smoother gradient of difficulty the tier they use is randomized between -2 and +2. -2 = 10%, -1 = 25%, 0 = 35%, +1 = 25%, +2 = 5%.“

So for your example. Phantom Train is base level 8, with the random level distortion could be level 10 (read about level distortion: https://wiki.ff6wc.com/flags/battle#scaling). Tier = enemy level / 5 = 2, with a 5% to be tier 4. So if Pearl is a tier 4 or lower spell then it certainly has a chance to use Pearl. We also don't know if the boss has any ”+ tier modifier“ (e.g whelk's shell counter in the above example has a +1 tier modifier).

The level scaling is the level enemies will actually be in battle (so it affects their damage calculations and ability scaling). First the exp/gp scaling type/factor is used to calculate the enemies level which is then used to scale their exp/gp. Then hp/mp overwrites that level based on its scaling type/factor and scales hp/mp. Level scaling will then calculate the final level and store it to be used for the rest of the battle.