For now Add-on Updater update must be applied manually if and only if you are using alphas or plan to test betas (there was an issue posted on GitHub where an alpha snapshot user found that installed add-ons stopped working after installing the latest alpha build, which is the correct behavior). For folks using NVDA 2021.3.4, you can either wait for Add-on Updater 22.03.1 to show up through Add-on Updater or install the new release manually, but eventually Add-on Updater will tell you that newer releases are available.
At one point I thought about checking versions in order to prevent people from downgrading. However I shelved that idea because different people use different versioning schemes, and this option isn't ideal for people using development versions of add-ons and/or using NVDA development builds.
As for Add-on Updater being integrated into NVDA Core, that will take a while as NV Access is researching some foundations for this suggestion at the moment. That's the major reason why I can't "graduate" from the community i.e. move on, knowing that Add-on Updater is a crucial add-on for users. Only after Add-on Updater becomes a feature in NVDA will I be able to say I can truly move on (there is one more thing I plan to submit to NV Access for inclusion in the screen reader, and that involves a feature in Windows App Essentials, and I plan to proceed with it in northern summer (June at the earliest)).
Hope this clarifies things.