Except for some maintenance stuff that you want to do on CLI as well, it is mainly for task that risk taking longer where you risk to into timeouts when running such commands over the webinterface. Especially for backup, updates and database operations this is the case, and if the script runs into a timeout, it potentially leaves your setup in a unusable state.
You could propose workaround in such cases, problem this is mostly an issue on webhosting. Unfortunately, these are probably the users the less experienced doing such stuff manually. And to be fair, you need to document and test all these procedures. On top of the general issues with hosting: How To: Get Help on Shared Webhosting
If it technically works (even with limits), I don’t think we should prevent users from using it (if they are aware of these limits). But it probably needs a few more experienced users like you, that help doing such things, document it, …