I never dabbled with the enemy scaling features of RPG Maker, but if it's possible I'd recommend having limited scaling instead of full scaling. In RPGs, players have levelling for the express purpose of being able to get overpowered. It might sound counterintuitive, but this is actually very important for the difficulty of the game. If a player has trouble with a boss, they have few options for beating it if they already are doing as well as they can strategically. As a result, levelling up beyond where a set-level boss expects you to be can be their only way to continue forward. That becomes impossible if everything scales forever. Furthermore, players in these games like to be able to go back to previous areas and feel the difference in their characters. To feel safe to engage with any threats because they're already past the levels of the area. That doesn't happen with full scaling. It's not good or bad, just a different way to do things that creates a different vibe. But it can lead to bad design if not handled carefully. Good luck!
I am glad you brought this up! I did not go into details in the post on how we will be implementing it, but we do intend to have a cap on zones and a set level for bosses.
For example, when the first few water zones comes out, it is intended for lvl 5 . If you just beat the candy factory and head straight there, the fights will be a breeze. Which is fine! But with the scaling we have in mind, the enemies would cap out at lvl 10. This makes em a bit more interesting to fight, but still easier and should give a strong feel of progression.
There will be a test out sometime soon when we feel like we are in a good spot. and would love feedback :)