According to the conditions, you can apply for PTRD only if you are outside the country without a valid PR, see here https://www.canada.ca/en/immigration-refugees-citizenship/services/new-immigrants/pr-travel-document/eligibility.html
you can receive your PR any time before your travel. Try to...
The point is that what you did during your master studies is generally considered a part from your duties as a student. The requirements of your master's program involved doing research and publishing articles, with or without a scholarship from your lab or professor. For example here in Canada...