You may try this:
toolbox create --image quay.io/toolbx-images/debian-toolbox:12
toolbox enter debian-toolbox-12
Than follow Signal instructions. You will have it installed, launch with signal-desktop. So you enter debian toolbox and launch Signal from it, that is Fedora atomic way.
I am not telling, that is 100% better, than Flathub version, but you may try just to see if problem is still there or not. Flathub version is also built from their debian file, it should be ok, but it also may contain some issues. If I would using Signal myself I would probably use Flathub, but if I had such issues I would definitly consider trying toolbox way.
Exceptions. Okey if I remember Firefox Desktop can set exceptions, so deleting data won’t delete exceptions? But Firefox mobile can not do it. That is what CookiesAutoDelete do, it manages exceptions, whitelist is not deleted, other cookies are deleted.
Or simple way (out of the box). Brave did it very simple with “forgetful browsing”, you check settings to delete every data by default, but with simple toggle you make exceptions-whitelist website, and this works very good for both desktop and mobile. You just never care about any cookies, but if you login to some twitter.com, you paste 2fa code, etc, you probably don’t want to do it 10x per day, just toggle “forgetful browsing” and it is done. That is about convenience.
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