Is there a ODIN or heimdall varient on Xperia? This one is what it says on the tin is there a form of ODIN and similar clients that have the capability to flash Stock and Custom ROMS to a Not boot loader unlocked device. I prefer if its built in Linux, but I don't mind using wine

Using Sony Xperia E C1505, android 4.1.1
Small note- if it relies on ro.product.name or the android version to detect a device,  no can do. I will accept universal flashing tools too.
Yup for Sony experia devices it is called Androxyde Flashtool 
-Flashtool is a software used to flash Sony [Ericsson] Xperia line (2010 to 2013) phones that use the S1 protocol

Please check http://www.flashtool.net to have more informations