Really confused as to how one of the most basic features in a server is so difficult to find and edit. I have been looking all over the web and in and out of files with no luck changing the php.ini values for sites on yunohost. Please get the documentation straighten out and get a definitive answer with a definitive process.
This warning indicates to packagers to not use php.ini and to use php fpm pool conf instead.
In a normal context yunohost user should not be obliged to change this kind of configuration. You could be in a specific situation or it could be a misconfiguration of the application you use. So please give a bit more context to let us evaluate the situation and may be create a fix on the app package, the yunohost core or the documentation.
About create a section in the documentation to explain how to change php configuration. I think it’s not really in our scope. I mean there is a lot of technology, yunohost install all of those technology (like php) quite commonly, the yunohost documentation could not be the documentation of all of these language.
But if you think to something specific, feel free to create a page on documentation (it’s wuite easy with the edit button) or a topic on this forum in the “Advanced use case” of this forum.