In my case, I didn't pay the fee yet, as I was informed that my scholarship will contribute to the tuition fee when I activate my scholarship after registering to the doctoral program. However, I still need to wait and see what IRCC thinks about this. I have explained about this in the letter of explanation as well.
Can you please share your experience regarding study visa process, particularly the proof of funding part? I'm in a similar situation as i have a funding letter from supervisor which clearly mentions the teaching assistantship and research assistantship that I ll be receiving for the entire duration of the PhD