https://www.pedneur.com/article/S0887-8994(15)00112-5/pdf
http://www.ajnr.org/content/27/9/1919
There seems to be a literature on use of MRI to confirm the diagnosis of encephalitis in children. Note the above article(s). I am googling MRI childhood encephalitis. There is more if you choose to look.
I am reading again your post where you say he had the normal MRI. Which is certainly a good thing. I am wondering whether when they do an MRI with suspected encephalitis if there are specific areas of the brain that they look at, that need to be illuminated and/or a specific point of attention, not typically investigated in a "regular" MRI.
The thing is, the doctors are not stupid or malicious. There may be a motivation within the Canadian system of medical care to avoid costs; but that the physicians be involved in a conspiracy to avoid certain diagnoses seems over the top.
But the thing is in the USA there are very strong biases in diagnoses, which out of the blue come to be "seen" everywhere for motivations that are not necessarily pure as the driven snow (think ADHD, or even Bipolar in children) and other diagnoses that are avoided at all costs (say autism that could be related to immunizations.)
I will leave it with you, what you do with this. Take care.
