I don't quite understand what you mean with "settings get inherited" regarding the languages there, since I'm just assigning the siteaccess "por" to a group which per se does not itself have any language assigned (I commented that setting for the group), thus, I figured the individual siteaccess setting "languages" for one particular siteaccess only only would apply (which is por-PT).
Ah, yes, I see that in posted config you've commented out site_group.languages. This is also correct setup.
Hmm, I'm running out of ideas of why I can't reproduce this.
I've just successfully tested this on Apache 2.4 and PHP 7.1.8 (via php7.1-fpm) with SYMFONY_ENV=prod and SYMFONY_DEBUG=false and immediately after executing attached testSystem:ezp27417:deleteTranslations command I got 404 for /por/MyTestEn.
I tested this on both Content Types: Folder (disabling always available before creating content) and Article (which has always available disabled by default).
6. I created an article "MyTestEn" on eng-GB language then translated it to por-PT, keeping the same name;
The DB dump you've sent me contains Folder of that name, not an Article, however Folder also has alwaysAvailable disabled there (which is not a default setup). The question is when did you disable it - before or after creating content?