Just as a quick update, we are proceeding to develop Endless OS 4, likely to be released within the next few months.
For this version, we have undergone the distro maintenance improvements I described above, and as such we now have the latest podman from Debian (3.0.0-rc2) plus toolbox-0.0.99.
There are some awkward details there meaning that upon upgrade, all previous containers stop working and need to be recreated 
we will document this in the release notes.
We also opened up our development ostree and I just published steps how you can try it.