I've never understood why storage varies out of the box with the same OS installed on the exact same model. For example why does the OS take up more storage on a 128GB 6S Plus as opposed to the OS on a 64GB 6S Plus taking less? Does anyone have the explanation for that?
It also has to do with formatting. The bigger the drive, the more storage you will lose due to formatting. Formatting usually decreases capacity around 8% (maybe a little more) off of the box.
So a 64GB storage module will lose less capacity than a 128GB because it's smaller.
8% of 64 is 5.12
8% of 128 is 10.24
So a 64GB device is working with about 59GB after formatting, and before the OS data is put on the phone, which is roughly accurate as the devices have about 55GB of usable space on first boot.
A 128 GB device is working with about 117GB after formatting, which is probably too generous - it's like about a GB less. This would line up decently well with the 112GB figures after first boot.
Then you have to factor in how files are allocated. Space can be wasted if you have a ton of tiny files on a FS with large allocation units. For example, on a Windows NTFS formatted drive (4KB AUs), a 1 byte file will still take up 4KB of disk space.