2 cents worth ... from personal experience ...
The web based update of plugins can bite ... depending upon what plugins you are updating/upgrading .... size of plugin (got one that is absolutely necessary [auth] and it's 22 Megs in size all the time). Had to increase php settings to get that one to complete.
Case two ... themes ... some themes are very heavy processing wise ... Essentials is an example. There are over 600+ settings to that theme. You upgrade a moodle and one of the first things one will notice is a notice from Essentials saying you must upgrade ... period.
Then there is Case three ... when updating via Web, the suggestion is made to install all upgrades. Catch 22 *IF* Essentials is one of those and it introduces some new dialog boxes/settings that's massive ... compared to the other addons one has upgraded.
Lethal combo for me ... the auth plugin that is large all the time + Essentials .... I do all other updates first, then the auth plugin and I save Essentials for last.
Yes ... could acquire the zips and do it manually ..... and yes, if I could find the proper git url for 'stable' and not experimental ... could do the git thing for all of them.
Mdeploy, which is what the web based updates are called, also changed where/what it did in the middle of a series (about 3.3 or so). At one time, the downloaded files and work area was in code directory. Has since been moved to moodledata ... which should mean it's safer in light of moodle security standards.
Me ... am a little lazy ... still use the Web based but it's nice to know, that If I had to, could complete a putzzed update/upgrade to a plugin via command line ... just have to figure out at what stage it hickup'd ... and have had to do that very thing with that auth plugin and Essenntials ... more than once! :\
So ... pick your poison! ;)
'spirit of sharing', Ken