Most projects follow the X.Y.Z versioning scheme, where:
X: Major version number, incremented for BIG updates/changes
Y: Minor version number; odd numbers are development versions, even numbers are stable/release versions; numbers are incremented for feature changes/additions
Z: Micro version number, incremented for bug fixes
So, versions 4.1.x and 4.3.x are development builds. 4.1 is no longer being worked on, as it became 4.2 when it became stable. 4.3 will become 4.4 when it becomes stable. Tvheadend also appends release and commit numbers to the builds, where 4.2.2-235-g10c0eca means version 4.2.2, release/build 235, made from git commit 10c0eca. If you don't want to be using unstable/development software, stick with the 4.2 series until 4.4 is ready.
As far as upgrading (or even downgrading), Tvheadend will happily use your existing configuration, regardless of whether it is installed with a package manager or manually. (Or a combination: I manually build Tvheadend, but package it into a format for my distro's package manager.)