In #334 we were using COMPOSE_FILE env-var, same as -f/--file cli arg to use multiple compose files in our profile folders (explicit, study, suite, ...).
Problem: the bind mounts path to local paths is sensitive from where we do the docker compose ... commands (look with docker compose config).
Solution: the include feature (howtos) since Docker Compose v2.20.0 permit to modularise file with the paths always resolved from the yaml where it declared, not from the current directory (pwd).
Verifying:

# from deployment/docker-compose/explicit-profiles
git checkout main
docker compose --profile all config > explicite.before.yaml
git checkout rework-compose-files
docker compose --profile all config > explicite.after.yaml
diff --color <(yq -P 'sort_keys(..)' -o=props explicite.before.yaml) <(yq -P 'sort_keys(..)' -o=props explicite.after.yaml)
#rm explicite.*.yaml

The config files has also been reorganized per service for easier management.

I also use this version since two months now without problems.