This depends on the implementation, if you replace template blocks using hivepress/v1/templates/{template_name} hooks or via another method instead of editing the theme or plugin files directly, then these customizations will be safe from updates.
Yes, we plan to make Messages more chat-like but there’s no ETA for this yet.
Yes, if you’re familiar with coding the best way is creating a custom extension, you can check our tutorial in the Developer Docs - it shows creating a custom URL, page with a custom template, etc. For real-time messaging you’d have to choose some solution not based on PHP (maybe Node) or embed a third-party service API for this.