I use a combination of netbox for the physical/logical network and server connectivity, and outline for text documentation of the different components.

This may be overkill for most use cases but you can use jcr.

The best reason to use it in my book is the garbage collection as the official registry doesn't have that feature and can and will bloat over time.

You should look into GrapheneOS if you're set on using pixel.

You may want to give this a quick read before using signal

https://dessalines.github.io/essays/why_not_signal.html

I personally haven't verified the claims on there but I've been using a personal instance of Matrix for a while now and it's been working great.