Simulated Open World VS True Open World VS Linearity?

[Koh]

So this is a game design question my partner and I are thinking thoroughly about.

The way I envision the World of Chaos games is that they are games that have a main focal story, but also several side stories revolving around the main, secondary and tertiary characters, so people can get involved with the inhabitants of the world and get attached to them. This also calls for many optional areas and dungeons in the world, but some places would need to be accessed later. However, I also want points in the main story where there will be a handful of areas to do at once (like 3+), requiring the player to choose the order, but all need to be done before moving on. The problem all of these key traits creates is level scaling.

My general idea to handle that is to make it so when players start a story for these areas, the game saves that, and uses it to upscale the enemies for the other areas, and when the player starts the story of another area, the game upscales the other areas that still need to be started as well. My friend Josh, however, has stated that this creates a problem of the player being locked into a section unintentionally; it'd punish the players who decide to check out an area for a few minutes, decide they want to come back later and go to a different area, only to find the monsters are much stronger, and can't progress through. I'm not, however, seeing why this would be such an issue, or a different resolution to the problem.

I simply do not want the game to be extremely linear, where the player doesn't have ANY choice in the order of some areas. I do, however, also want later areas to be scaled up in level so that the player will still have a challenge after finishing one of the handful of areas. The whole game, besides the main story, is also about exploration, so I want players to be able to actually explore with some free will.