The problem with some themes and plugins is that updates only show up after another component is updated. For example Avada theme has 2 plugins dependent on the theme, and updates are available to them only after the theme is updated. Some other themes and plugins have the same issue: available updates show up after other updates, so they won't be updated with a single run. It would be good to have at least the option to have plugins updated twice, with a check if new updates are available after the first plugin and theme update. In this case, with Avada, the problem is probably the worst (not including rare cases where something breaks) because there is always a big warning in admin after updates, because those two plugins have to be updated after the theme.

Not sure if you use wp cli or something else, but with cli, the loop would be like this, for example:

plugins

wp plugin update --all

themes

wp theme update --all

core

wp core update

refresh update information

wp eval '
wpcleanupdatecache();
wpupdate_plugins();
'

plugins that were dependent on other updates, if there were any

wp plugin update --all