Clean install- erasing disk vs erasing volume
A discrepancy between the drive size and the size of the boot partition is not unusual. Some of this missing space is consumed by the following:


The hidden Recovery partition
The hidden EFI partition
Space used by the file system on the OS X partition
Space used by Core Storage (This is optional depending on your Macs
hardware)


When you have booted from the flash drive, you can erase your disk to maximize the OS X boot partition space by repartitioning the drive. You should create a single "Mac OS Extended (Journaled)" partition. The required hidden partitions will be created automatically. If you have single SSD drive, then you are not required to use Core Storage unless you need encryption.