With no photos, this is just a "shot in the dark"...pun intended.

What if you reversed the plan and had bed on the floor?

If it is too late to to reverse continue on with this plan for ceiling box and fan.

https://www.amazon.com/SYLVANIA-General-Lighting-61403-Recessed/dp/B084YCJ1CY/ref=sr_1_5?c=ts&keywords=Recessed+Light+Fixtures&qid=1692049980&refinements=p_n_feature_thirteen_browse-bin%3A5693063011&s=lamps-light&sr=1-5&ts_id=3736711

Then I would replace the fan with a blade-less profile fan, sized to the room (around 25")

https://www.amazon.com/Ceiling-Control-Profile-Dimmable-Bladeless/dp/B09Y257TZR

1. What is a "low cock loft"?
2. What are the dimensions of the loft and how high is the ceiling above the loft?
3. How does one reach the loft? Fixed staircase, movable ladder?
4. How are the main level and loft furnished?
5. Are there wall outlets on the main level? In the loft area?

A junction box can be moved but maybe at least post a pic of the space so we have a visual. BTW I would never do a fan in a space with bunk beds . Yes you could do a track but the junction box will still be where the track attaches to the wiring. I honestly cannot understand the issue with 9' ceilings , go led bulbs they do not get hot and run the track as far away as possible from the bed .

Lighting from a single source is kind of harsh, especially in a bedroom. I would plan for some portable lamps like a floor or table lamp, a desk lamp and a pin up sconce for the bed

Lights should be placed where they are needed. Consider using wall sconces.

Please post a few pics of the room, door placement, closet placement, window placement. Also sketch indicating dimensions so that we can layout and properly advise.