You could also just run IMAP/JMAP/SMTP as separate components, I can't see any place in the Stalwart documentation - or in the Docker image itself - where monolith is the only option.
I haven't tested the setup myself yet, but me and another root are planning on testing a setup of Stalwart to replace a semi-broken IMAP/JMAP setup for a computer club, keeping the SMTP as is.
I personally use ~/.bin for my own symlinks, though I also use the user-specific installation instead of the system-wide one.
I wouldn't guarantee that any automation handles ~/.local/bin or ~/.bin either, that would depend entirely on the distribution. In my case I've added both to PATH manually.
Flatpak already creates executable wrappers for all applications as part of regular installs, though they're by default named as the full package name.
For when inkscape has been installed into the system-wide Flatpak installation, you could simply symlink it like; ln -s /var/lib/flatpak/exports/bin/org.inkscape.Inkscape /usr/local/bin/inkscape
For the user-local installation, the exported runnable is in ~/.local/share/flatpak/exports/bin instead.
The official binhost project has been an experimental thing until now, I've personally been using it for the year on multiple machines, but it's not been something that you can just enable. And it's definitely not been something that's come pre-prepared in the stage 3.
Flatpak uses OSTree - a git-like system for storing and transferring binary data (commonly referred to as 'blobs'), and that system works by addressing such blobs by hashes of their content, using Linux hardlinks (multiple inodes all referring to the same disk blocks) to refer to the same data everywhere it's used.
So basically, whenever Flatpak tells OSTree to download something, it will only ever store only copy of that same object (.so-file, binary, font, etc), regardless of how many times it's used by applications across the install.
Note that this only happens internally in the OSTree repo - i.e. /var/lib/flatpak or ~/.local/share/flatpak, so if you have multiple separate Flatpak installations on your system then they can't automagically de-duplicate data between each other.
A lot of that data doesn't actually exist, ostree hardlinks data blobs internally, so the actual size on disk is much smaller than most disk usage tools will show.
Probably not what you're looking for, but I'm going to note that Turris make some great OpenWRT routers.
Currently running theTurris Omnia, and using both Wireguard and Yggdrasil through it.
I've been personally using KDEs Itinerary app, but it might not be what you're looking for
A.k.a. do you have a larger version?
Haven't really used any proper JMAP clients - since the setup is broken anyway, so mainly just curl.