It will come with the latest CME version if you order it Cisco direct. If you get it through a Cisco partner, they may get it eitehr Cisco direct or distribution and if you get their professional services, they will get it upgraded to the latest and greatest CME version.
The firmware files do come in flash, but if you have a particular phone firmware that you need, you can always download it from CCO Software downloads.
There is no license enforcement in CME, but you have to buy a license per phone. The part number is SW-CCME-UL-79XX. Where XX can be 60,40,61,71,70,11,12,05,02 etc depending on the type of phone you buy.
Hope that helps
Sankar
PS: please remember to rate posts!
Sankar Nair
UC Solutions Architect
Pacific Northwest | CDW
CCIE Collaboration #17135 Emeritus