Are en-route masters in physics viewed differently from terminal masters in physics in the Canadian job market?
My understanding is that an en-route masters is simply a masters awarded with an understanding that the person will also continue onto a PhD. I don't think this assumption/understanding makes it any less of a masters. In other words, the masters is not conditional on work done in the PhD. My impression is also that the person would have needed to do several significant things to get the en-route masters, and the magnitude of those things is likely similar to the person who got a terminal masters.

So, no, I don't think en-route is viewed differently in general. 

Note that I am Canadian.