Is it ok to update FreshRSS from within the software itself (it says version 1.21 is available and that I can download it) or should I wait for the YunoHost package to update?
I believe it is disabled and won’t work from inside the software.
You shouldn’t do it anyway, except if you really know how to manage it.
You are welcome to try the upgrade if you like to : Testing : upgrade to 1.21.0 by lapineige · Pull Request #161 · YunoHost-Apps/freshrss_ynh · GitHub yunohost app upgrade freshrss -u https://github.com/YunoHost-Apps/freshrss_ynh/tree/testing. We actually need testers to release this new version 
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Testing now! Thanks so much.
What’s the result ?
Everything’s working as it should, at least as far as I can tell.
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Great !