The ticket will not be fake when you install legit cia and thats the point.
The ticket will be clean, because it´s properly signed by Nintendo.
Your 3DS behaves as if it the software was officially preinstalled.
About system transfer and preinstalled software:
If you choose to delete the content off the SDHC Card or microSDHC card, such as during a system transfer, the pre-installed game will be available for redownload from the target system's Nintendo eShop after the transfer has been completed.
http://en-americas-support.nintendo.com/app/answers/detail/a_id/14143/p/430
Regarding system format with preinstalled software:
http://en-americas-support.nintendo.com/app/answers/detail/a_id/166/p/430
Preinstalled software is not listed there.
I
think the ticket of the legit cia won´t be deleted from the console during a system format.
The eShop checks if you have a legit ticket installed and lets you redownload the software.