OK @garrett , I understand.
Your previous passbolt v2 install script delivered a .htaccess in the webroot folder, containing instructions for apache about rewrite rules :
RewriteEngine On
RewriteCond %{REQUEST_FILENAME} !-f
RewriteRule ^ index.php [L]
Basically, it says : “if you don’t find the requested URL directly, pass it as an argument to index.php”
Your deb installer does not deliver this file anymore.
I’ve manually added those lines in my configuration file. It works now 
Thank you for your help, sharing my blurry thoughts with someone else definitely helps to solve the situations quicker !
Regards,
farfade