I think the bigger question is that if indeed Nico G is not for sale and the club have never had any intention of selling him then it is baffling that Guardiola is not giving him any minutes ahead of players who will end up leaving the club.Hopefully we can put these rumours to bed now, and see how he develops as a player in his first full season at the club.
The club coming out to shut down the leaving rumours does nothing to quell the fact that Guardiola sees Nico as seventh choice central midfielder as evidenced by his amount of game time. The worst case scenario and what I think it looks like from the outside looking in is that the club want him stay but Guardiola doesn't think he is good enough and wont play him if he has a choice. I know Pep is a genius but surely it is more beneficial to give more time to the players staying than those leaving.
I think you could rinse and repeat the above for Khusanov and potentially Reis but they both have the excuse of being teenagers or just turning 20 so their lack of game time is a bit more acceptable. However if Akanji, Stones, and Ake dont leave then the two of them will be 6th and 7th choice centrebacks and for their development they just wont get enough minutes.