When I posted this question some of the members of the community suggested I should extract this particular point into another question so everyone could weigh in.
In this network comments are handleded in a stricter way than in other Networks. This makes people confused, because they think they are doing everything as they always did, so their comments should be accepted, and they fail to realize that in other Networks moderation of comments is more lax and their comments were actually against the rules.
However, people, as general rule, are here to help. Any time I wrote a comment in no way I was doing it to troll the other person, whether the comment was following or not the rules of the network I meant it well. So having your comments so consistently deleted without even an explanation or only the very cold "comments are not for extended discussion", when in other Networks this is handled totally different can be extremely shocking. In other networks you get the "extended discussion thing" when there are 20 comments or more, so you easily understand it and even feel a tad guilty. Here I have seen it happen with 3 or 4 comments.
I think we should update the message "comments are not for extended discussion" to something along these lines to help users understand better why their comments are being deleted here while maybe they wouldn't in other sites:
In IPS we follow closer the rules for comments, please read them here. Comments shouldn't be used for extended discussion, if you wish to discuss further with the OP you can open a chat. Please read here for more details on why we do this. Thanks a lot for your collaboration!
I picked two links that I think could work, but I am open to any suggestion on the wording and links to be used.
PS: I am not native English speaker so I am sure this wording can be greatly improved. I am open to any suggestions.