As far as I can tell, yes, it is.
Showing a universal Turing machine is a proof of the fact that when you write stuff like the smn theorem or anything that uses universal functions you aren't writing nonsense.
There is no "contract" between the universal machine and the hypothetical user. One could certainly ensure that, say, the input TM is properly formatted, or that "the runtime" will only use a certain set of cells, and so on. The difficulties and problems one would find in trying to do so are the same one would face when writing an operating system and a compiler.