It should be quite usual situation when you need to adjust your server’s php upload limits (or other parameters). I had some experience with apache and remember finding many different instructions how to do it, some of which worked and some didn’t. I don’t want to experiment again on production server now.
Maybe it is a good idea to ask for recommendations here and leave them in written for others.
So, I expect there should be two basic use cases: global PHP settings for all yunohost needs (we probably shouldn’t even touch it, right?) and per-app settings. So, what is the safe way to tune PHP in Yunohost?