Not missing anything. We just see it differently.
Any accused has the right to put his best foot forward. In the case of Fortin, he was charged as a soldier committing an offence against a fellow soldier in a military environment. Victims' advocates then bleated that "the use of military dress was a form of intimidation and bullying." That's pure horseshit and is an interpretation of the wearing of a uniform that ought to be offensive to any serving member.
IMHO, the CoC regretfully bought into that argument. I expect that they also bought into the idea that an accused wearing a uniform in a public court is "bad advertisement for the brand". That's where the presumption of innocence comes in. If one really believes in the presumption of innocence then the uniform in court has zero consequence and should be treated as a routine. Suppressing the wearing of the uniform in these circumstances is taking sides.
Let me make it clear. In my humble opinion if a soldier is charged with selling drugs downtown then he goes dressed as a civvy. No question in my mind. But where its really something which, like this, is at its heart a military matter directly impacting service discipline then people should appear "on duty" and "in uniform".