In my environment, the number one reason Apptainer is used has nothing to do with deployment, isolation, or software availability: it is to work around inode limits.
On our HPC cluster, each user has a quota of inodes on the shared filesystem. This makes installing some software with lots of files problematic (like Anaconda). An Apptainer image is a single file on the filesystem though (basically squashfs) so you can have those with as many files as you want in each.
Installing the same software normally is easy and works fine though, you just exchaust your quota.