[cli] Fix regression preventing --config from overriding default kibana.yml - #155436

## Summary
Fixes: #155154 (introduced in #149878), builds on #155436 .

- Adds tests to ensure the configuration merging order, check those for
reference.
- Updates the README to explain the intention
 
For the tests, I needed to output something to the logs. I hope it's not
a big issue to log it. If needed, I might hide that behind a verbose- or
feature flag.

### Checklist

- [x] [Unit or functional
tests](https://www.elastic.co/guide/en/kibana/master/development-tests.html)
were updated or added to match the most common scenarios

---------

Co-authored-by: Kibana Machine <42973632+kibanamachine@users.noreply.github.com>

## Summary
Fixes: elastic#155154 (introduced in elastic#149878), builds on elastic#155436 .

- Adds tests to ensure the configuration merging order, check those for
reference.
- Updates the README to explain the intention

For the tests, I needed to output something to the logs. I hope it's not
a big issue to log it. If needed, I might hide that behind a verbose- or
feature flag.

### Checklist

- [x] [Unit or functional
tests](https://www.elastic.co/guide/en/kibana/master/development-tests.html)
were updated or added to match the most common scenarios

---------

Co-authored-by: Kibana Machine <42973632+kibanamachine@users.noreply.github.com>
(cherry picked from commit c57589e)

# Backport

This will backport the following commits from `main` to `8.8`:
- [Fix config stacking order
(#158827)](#158827)

<!--- Backport version: 8.9.7 -->

### Questions ?
Please refer to the [Backport tool
documentation](https://github.com/sqren/backport)

<!--BACKPORT [{"author":{"name":"Alex
Szabo","email":"alex.szabo@elastic.co"},"sourceCommit":{"committedDate":"2023-06-05T13:15:07Z","message":"Fix
config stacking order (#158827)\n\n## Summary\r\nFixes: #155154
(introduced in #149878), builds on #155436 .\r\n\r\n- Adds tests to
ensure the configuration merging order, check those
for\r\nreference.\r\n- Updates the README to explain the intention\r\n
\r\nFor the tests, I needed to output something to the logs. I hope it's
not\r\na big issue to log it. If needed, I might hide that behind a
verbose- or\r\nfeature flag.\r\n\r\n### Checklist\r\n\r\n- [x] [Unit or
functional\r\ntests](https://www.elastic.co/guide/en/kibana/master/development-tests.html)\r\nwere
updated or added to match the most common
scenarios\r\n\r\n---------\r\n\r\nCo-authored-by: Kibana Machine
<42973632+kibanamachine@users.noreply.github.com>","sha":"c57589ec57e5e8265a66cd9c8c2102005736f6d8","branchLabelMapping":{"^v8.9.0$":"main","^v(\\d+).(\\d+).\\d+$":"$1.$2"}},"sourcePullRequest":{"labels":["Team:Operations","release_note:fix","backport:prev-minor","v8.9.0"],"number":158827,"url":"https://github.com/elastic/kibana/pull/158827","mergeCommit":{"message":"Fix
config stacking order (#158827)\n\n## Summary\r\nFixes: #155154
(introduced in #149878), builds on #155436 .\r\n\r\n- Adds tests to
ensure the configuration merging order, check those
for\r\nreference.\r\n- Updates the README to explain the intention\r\n
\r\nFor the tests, I needed to output something to the logs. I hope it's
not\r\na big issue to log it. If needed, I might hide that behind a
verbose- or\r\nfeature flag.\r\n\r\n### Checklist\r\n\r\n- [x] [Unit or
functional\r\ntests](https://www.elastic.co/guide/en/kibana/master/development-tests.html)\r\nwere
updated or added to match the most common
scenarios\r\n\r\n---------\r\n\r\nCo-authored-by: Kibana Machine
<42973632+kibanamachine@users.noreply.github.com>","sha":"c57589ec57e5e8265a66cd9c8c2102005736f6d8"}},"sourceBranch":"main","suggestedTargetBranches":[],"targetPullRequestStates":[{"branch":"main","label":"v8.9.0","labelRegex":"^v8.9.0$","isSourceBranch":true,"state":"MERGED","url":"https://github.com/elastic/kibana/pull/158827","number":158827,"mergeCommit":{"message":"Fix
config stacking order (#158827)\n\n## Summary\r\nFixes: #155154
(introduced in #149878), builds on #155436 .\r\n\r\n- Adds tests to
ensure the configuration merging order, check those
for\r\nreference.\r\n- Updates the README to explain the intention\r\n
\r\nFor the tests, I needed to output something to the logs. I hope it's
not\r\na big issue to log it. If needed, I might hide that behind a
verbose- or\r\nfeature flag.\r\n\r\n### Checklist\r\n\r\n- [x] [Unit or
functional\r\ntests](https://www.elastic.co/guide/en/kibana/master/development-tests.html)\r\nwere
updated or added to match the most common
scenarios\r\n\r\n---------\r\n\r\nCo-authored-by: Kibana Machine
<42973632+kibanamachine@users.noreply.github.com>","sha":"c57589ec57e5e8265a66cd9c8c2102005736f6d8"}}]}]
BACKPORT-->

---------

Co-authored-by: Alex Szabo <alex.szabo@elastic.co>