So yes, you can't modify the actual embodiment of the state transition if it does not offer you the capability to do so. But as long as it interprets data in a TM manner (input and output are colocated and the alphabet is the same), you can write code that will interpret data as code and manipulate code as data. Not by modifying the base substrate, but by adding a virtualization layer on top.
Everything else is data.
By the time you get to programming language like C and LISP, and software like vim or firefox, everything is abstracted away and the only limits are self-imposed (or imposed by others that have done the work). They are not laws of nature.
So yes there’s a definition of code and data. But for the Turing machine, there’s only the tape and its content.