In Oracle, why would I not always delete all old archive log files with RMAN? backup archivelog all delete all input;


I do not understand why you would not always do this.  Why would I only want to delete archive log files from one location?

When Oracle saves the archive log files to multiple destinations, am I correct they are all duplicate and exactly the same in each location (and thus why the all vs not all)?
Yes, archive log can duplicated in multiple locations, and in many cases delete all is what you normally do. 

But sometimes you may want to control one or more location without rman. For instance, Data Guard is not available in Standard Edition.   However, couple simple shell scripts can replace it to some extent . Surely, it's not a full substitution, but it's enough for most small-to-medium systems that use Oracle DB .  All you need is to reliably copy archive logs from one host to another, and restore them.  It's much better to give full control over one of archive log destinations to these scripts (or maybe homebrew applications or third party products) , so they can decide when it's safe to delete them.