Hi DenisIaq,
I downloaded your project and started processing with what seems to be a promising workflow, but there are so many images that I'm not sure it's going to finish before tomorrow!
So anyway I can tell you what I did so you can try it if you like.
As Bzuco noted, a lot of the images in Copy of Chunk 2 did align reasonably well, though it's hard to tell because they are dwarfed by a smaller number of very poorly aligned images which throw the scale way off.
I didn't look in any of the other chunks.
I figured that you had converted 360 images to cube faces, so I got an AI to write a python script to set each set of cube faces to a station camera group. see camgroup.py attached. This tells metashape that these image share a 'nodal point' (this might be the wrong term but i know what i mean) and the images are forced to be located at the same spot.
I selected all images and right clicked -> reset camera alignment. Then I tried just aligning the first 50 or so images (select ~50 sequential images in the photos pane and right click -> align selected cameras), and they aligned pretty nicely.
I then selected a load more and repeated, and they aligned nicely to the previous ones.
I did a bit of gradual selection to remove bad points and ran optimise and wondered if it was valid for all images to share a single calibration group as they would have been cropped from different parts of the 360 image and so it might be more appropriate to calibrate them according to which part of the 360 they were cropped from.
The AI struggled a bit with that script, and it's not great, and i didn't spend any time improving it, but it works for now - calibgroup.py attached.
I don't know if that actually makes much difference, but it assumes that all images suffixed with _0 are from the same part of the 360 and same for _1, _2 etc and creates calibration groups for each. you can see the calibration groups in tools -> camera calibration.
I then continued aligning additional batches of images, occasionally doing a gradual selection and optimise, until i got up to ~600 aligned images, with still most of 5000 left.
At that point I got it to align all the remaining images, and that's what i'm waiting for now.
As Bzuco points out it's not an ideal camera and the white surfaces won't help much with reconstruction, but the alignment might come out ok.
I would also suggest massively reducing the number of photos, at least initially just to check that you can get a good alignment. I think you could just keep every 5th set of cube faces so you have more like 1000 images and you'd still have enough overlap for alignment.
I'll let you know tomorrow if the alignment completed this end, and share the result if it's not awful!