They are processing your applications because, now that your eligibility for citizenship became out of question, it’s an opportunity to take in the processing fees and encourage you to remain invested in Portugal.
As I have read in depth about the Portuguese GV in the years prior, it bears all the hallmarks of a classic Ponzi scheme. At first, it’s so easy and some GV holders do in fact become citizens but it’s a small number. Next, it attracts attention and tens of thousands apply so they stop processing leaving people waiting but at the same time approving just a few not to kill hope and keep investor money flowing. A few years go by and investors realize the game, they resort to lawsuits and the GV program gets a bad rep turning new investor money away. So they come up with novel idea, no no they wouldn’t process your applications as they were supposed to, they will now just “count” your time differently from the time when you applied so you would think you’re already making your way in the queue towards citizenship when in fact you were not admitted into the country. You think they excluded the GV PR by accident? No! They excluded it because that would’ve allowed you to liquidate your investment making a loophole in their scheme. Now the next stages of their scheme is that they will extend the time for PR, possibly in two or three years but some will get it but the masses won’t. The citizenship will remain 10 years (Portugal signed a convention regarding this limit), and some committed investors will actually acquire it but in just the right time they will introduce physical residence requirements to it so that the masses will be excluded once more even if they hold GV PR. If you think that in the year 2036 a first world country still grant its citizenship to foreign nationals who do not live there you are mistaken. Even if some large number of GV holders do reach the citizenship application stage, they can just shelve them and leave them waiting. And if they were forced to make a decision they can just claim you have no connection to the country and refuse your application
Bottom line is you cannot buy your way to EU or in any of the first world countries, at least not with Portugal. If you happen to like investing there then go for it, otherwise avoid investing solely for the reason of acquiring citizenship.