My experience is somewhat different: I went to get my fingerprints taken to obtain the US police certificate, I was asked why I was requesting it and I stated "to apply for Canadian Citizenship", and this is what was written in my fingerprints card.If your RQ/CIT0520/CIC letter is not submitted during your fingerprinting, the agent will not fill that section out with "CIC or Citizenship" but rather with "I-PR". I forgot what that stood for but I'm confident it's something along the lines of "personal request". You'll still get your certificate, but you want to be sure of 2 things: 1- that the CIC IO will accept it, and 2- that the date the background check is completed can fall after the date CIC requested it. I did exactly that despite the agent warning me about it (certificate was from greece). Where I got incredibly lucky was that they were so backlogged in greece that by the time they started processing my request I had already done my interview.
If you choose to wait for CIC to request it, send them a letter a week or two later explaining that you have made the request, with a copy of the fingerprinting receipt and the form/tracking number. They only give you 30 days to present it but it takes a little longer.
Therefore what you say regarding the absence of "RQ/CIT0520/CIC letter" being a problem is unlikely to be true. Furthermore, if I know I have stayed more that 183 days in a foreign country and I know I have to submit a police certificate, I will do that together with my original application, when it is obvious that I have no letter or request of any kind from CIC because they are not psychic and do not know that I want to apply for citizenship. This makes all your points rather moot: if you include the police certificate in your original application, CIC should really accept it, unless it is deemed to be "too old", i.e. dated months in advance of the application date.