Enemy ability scaling is based on two main factors: vanilla abilities and monster level.

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.