[EDIT: site worked for "a few minutes"]
@Hypolite Petovan

local.config.php

'config' => [
                  ],

        'system' => [ 
                'urlpath' => '/var/www/subdomaincom/',
        ],

bin/console config print, the order of the lines is different!

system.url => https://sub.domain.com
system.php_path => /usr/bin/phpX.y-fpm
system.urlpath => /var/www/subdomain/
system.ssl_policy => 1
system.basepath => /var/www/subdomaincom

Site doesn't work, resulting in the screen as shown in the initial post.

Setting the URL as described:
/var/www/subdomaincom/bin/console config system url https://sub.domain.com
.. the site works for a few minutes.

@Hypolite Petovan

local.config.php

'config' => [
        ],

        'system' => [
        ],

bin/console config print, this time one of the references doesn't show up anymore:

system.theme => frio
system.url => https://sub.domain.com
system.php_path => /usr/bin/phpX.y-fpm
system.ssl_policy => 1
system.basepath => /var/www/subdomain

@Hypolite Petovan

Couldn't find any relevant setting or hint in static/defaults.config.php searching for the term path.

I did (again) a diff check of the print of bin/console config of the two subdomains.

The domain that doesn't work still displays the setting;
config.system.basepath => /
.. and I have no idea how to delete/ erase the /

The subdomain that works has the following line that doesn't show up in the one that doesn't work:
system.urlpath => /var/www/sudbomain2/

@utopiArte Sorry, I was on mobile and couldn’t check but these keys should have been mentioned in this file, along their purpose.

system.basepath is the absolute file path where Friendica is installed, e.g. /var/www/subdomaincom in your case.

system.urlpath should only be used if Friendica is installed in a subfolder of the domain you’re using, and is relative to that domain. It doesn't seem to be relevant to you, so it should be blank.

system.url is the absolute URL where your Friendica node is accessible. It should consist in the protocol, the domain and the urlpath together. In your case it should be https://sub.domain.com/

system.php_path should be the absolue path to the PHP CLI executable. It should not point to PHP-FPM, which is used to process web requests.

@Hypolite Petovan

It should not point to PHP-FPM

Changed this setting in the local.config.php to phpX.y. The sites are working like before.

I decided to copy/paste identically local.config.php of the site that does work to the one that doesn't, only changing the specific detail of DB and folder structure, and also made sure that the .conf files are alike.
Still having the same problem.

Compared the print of:
/var/www/subdomaincom/bin/console config
in the few minutes it is working correctly after sending:
/var/www/subdomaincom/bin/console config system url https://sub.domain.com
and when it doesn't work but the prints are identically.

The print right now for both sites show the following quite at the bottom of the print:

system.url => subX.domain.com
system.php_path => /usr/bin/phpX.y
system.urlpath => /var/www/subXdomaincom/
system.ssl_policy => 1
system.basepath => /var/www/subXdomain/

The only difference between the two sites in the print is the following line quite at the top:
config.system.basepath => /
This line doesn't exist in the site that is working and I can't find a way to skip it or delete the /.
Meld (the diff program) shows a dot in front of the the slash ./, the simple text editor Kate doesn't.

Meld actually also shows the [enter] signs in the same way, a little bit less colored, in lines that have them, like it shows the dot.
🤷‍♂️

(notes (to myself))

hypolite wrote:

system.urlpath should only be used if Friendica is installed in a subfolder of the domain you’re using, and is relative to that domain. It doesn't seem to be relevant to you, so it should be blank.

hypolite wrote:

system.url is the absolute URL where your Friendica node is accessible. It should consist in the protocol, the domain and the urlpath together. In your case it should be https://sub.domain.com/