The levels of the Runic Island doodles are decided mostly by progression: the earlier a doodle appears in the island’s lineup, the lower its level, and the later ones are higher level. One wiki note says their levels vary based on how many doodles the Stone Guardian has, with the first being the lowest level and the last being the highest.

How it seems to work

From the available info, Runic Island uses a fixed, ordered scaling system rather than fully random levels. That means the designers likely assign levels by encounter order and difficulty curve, so each later doodle is meant to be tougher than the ones before it.

What players usually notice

A community video listing Runic Island evolutions shows many of the doodles evolving at set milestones like level 30, 32, 40, 43, 44, or 45, which fits the idea that the island’s doodles are built around a planned level progression rather than arbitrary values. One exception mentioned there is Griblow’s evolution, which requires level 45 even though the current cap was noted as 44 at the time.

TL;DR

So, in practice, the levels are decided by the island’s internal order and difficulty scaling, with earlier doodles lower and later doodles higher. The exact levels appear to be pre-set for each doodle, not randomly generated.