apt repository works for apt update, but symlinks are required to install, why?

I have an apt repository using an apache server at /var/www/organization.org/

the file structure is

.
+- Release
+- dists/
     +- stable/
     |     +- main/
     |     |     +- binary-all/
     |     |     |      +- Packages.gz
     |     |     |      +- package1.deb
     |     |     |      +- package2.deb
     |     |     +- binary-amd64/
     |     |     |      +- Packages.gz
     |     |     |      +- package1.deb
     |     |     |      +- package2.deb
     |     |     +- binary-arm64/
     |     |     |      +- Packages.gz
     |     |     |      +- package1.deb
     |     |     |      +- package2.deb
     |     +- contrib/
     |     |    +- [...]
     |     +- non-free/
     |     |    +- [...]
     +- testing/
           +- [...]
     +- unstable/
           +- [...]

And I have this in my source.list

deb http://server_url stable main contrib non-free

When I run

sudo apt update, things go smoothly.

When I do sudo apt install package_name, it cannot find any package.

It turns out that in the Release file, it uses this path Filename: /var/www/organization.org/binary-all/package_name.deb (missing dists/stable/main).

So when I add a symlinks like this binary-all -> dists/stable/main/binary-all/, I have no issues installing the packages. So everything works, but this is a hack which prevents actually working with unstable/ and testing/ folders because the symlinks are at the root besides Release and dists/.

This is the script that I use to generate Packages.gz and the Release file, which might be relevant.

#!/bin/bash

APT_REPO_DIR=/var/www/organization.org/
DISTS_DIR=$APT_REPO_DIR/dists

YELLOW='\033[1;33m'
BLUE='\033[1;34m'
NO_COLOR='\033[0m'

pushd dists
for stability_directory in */; do # Usually called: stable, unstable, testing
  echo -e "Indexing directories under ${YELLOW}$stability_directory${NO_COLOR}"
  pushd $stability_directory
  for license_directory in */; do # Usually called: main, contrib, non-free
    echo -e "Indexing ${BLUE}$license_directory${NO_COLOR}"
    pushd $license_directory
    for binary_directory in `find binary-* -type d`; do # binary-amd64, binary-arm64...
      dpkg-scanpackages $binary_directory | gzip -9c > $binary_directory/Packages.gz
    done
    popd
  done
  popd
done
popd
dpkg-scanpackages $APT_REPO_DIR | tee $APT_REPO_DIR/Release > /dev/null