Also I realized that
The REST API endpoints that create new Tweets (statuses/update) will accept a new boolean parameter when a Tweet is sent as a reply to a conversation: auto_populate_reply_metadata (true to enable, false to disable, false being the default). The existing in_reply_to_status_id must also be set.
It means that if we create a new tweet, that is not a direct reply to another one but we do use @mention at the beginning of the Tweet, it will be counted as part of the Content (140 characters).
If this is true, why such decision?