I also don't think it would've been too jarring to change the skybox mid-tunnel, but alas. My theory is that they used the Sector 6 skybox to give the lighting in Sector 5 a "source". For example, the sunlight around Aerith's house would look unnatural if the completed Sector 5 plate was above, which blocks out the sun.
Of course the better solution would be to use the correct skybox and just have Sector 5 be dimmer. I found Remake's interpretation far too bight (and far too brown).
I've been thinking of a quick fix since the PS4 days. My solution is to mirror the Sector 7 skybox as it's already capable of transitioning between midday and sunset, plus it has a nighttime variant. Then I'd just install the mod whenever I play Chapter 8. Maybe in a few years modders will develop a way to seamlessly load the two skyboxes in-game to alleviate the issue in Chapter 14, but for now I'd settle for fixing Chapter 8 just for the screenshots.