I have recently come across situations on this site that I would've liked to ask and bring up to SE managers/creators without it being to the public or raising a flag. I specifically would like to have a conversation with the SE about a specific question/user that has been deleted. Is there some way I can do this? If not, can I make a request for all users to have the option/a way of contacting SE?
The first order of business is to find if you want to contact site moderators or community managers. These are disjoint groups of people: the former are volunteers, the latter are employees of Stack Something.
Moderators can be contacted using a flag, or you may be able to catch them in a chatroom. If you want to ask about a deleted question, it's more likely to be a question for moderators than for community managers.
Community managers can be contacted using the bold link contact us in the footer of every page.
That said, don't expect
to have a conversation with the SE about a specific question/user that has been deleted
They don't have time for chatting in general, and do not disclose why a user was deleted for privacy reasons.