There's a number of mods that adjust the Joja prices down to actually make it a decision you have to think about. I don't play without one.
Lore-wise there's a bunch of dialogue that indicates that Joja pushes out local competition by offering prices far lower than what local shops can offer (see irl: Walmart), but it's not actually reflected in game through their prices.
In my opinion it's a glaring and weird oversight, considering the main thrust of the plot revolves around the conflict with Joja, but it's not ever a choice a player would make unless intentionally doing a themed/challenge/roleplaying run.