Sure, you can object that the encoding is "outside" the TM, but for the purposes of discussing complexity these objections are pretty trivial, again for the same reasons (whatever encoding you pick the conversion process is a program you can write down, and once you write it down it means the Kolmogorov Complexity is the same between different TMs up to the length of whatever encoding/decoding program you come up with).
Put another way, a TM with alphabet is {0, 1} is technically not the same as the TM with alphabet {A, B}. But it's obvious to us that the TMs are equivalent.