Thank you Legalfalcon!
I am no political expert but my understanding is that Canadian provincial governments are not necessarily subordinated to the federal government, but rather are considered co-sovereign.
PNP nominees are by no means already partially verified/ approved under the IRCC point of view. You show your interest to reside in a certain province so the province will nominate you - it is one of the ways to be qualified to enter the pool. Once you are in the pool and invited to apply, IRCC probably aren't too concerned with your stream but rather to focus on verifying your application. Please keep in mind that federal and province don't necessarily share or have access to the same information, therefore the need for IRCC to do their own verifying work.
Using a real-life example, I see it as some high school graduates go directly to university; some go into an associate degree program first then switch to university. There is no one way better than the others but choose the one that best suits your needs and situation.
Another conspiracy of mine is that people who directly apply to federal (CEC & FSW) meet the 'needs' of federal development of the country, whereas PNP meet only the needs of provincial development in the province. IRCC works for the federal so they want to take care of themselves first...
Just my 2 cents on why it isn't 'unfair' in IRCC point of view to prioritize streams.