Different messaging UI styles should be determined based on many criteria, and a seemingly simple visual change can affect how messages are grouped (or not), searched, and so much more.
In general, threaded/line-item style UI is ideal for longer-term conversations. The thread-centric design creates an opportunity to efficiently collaborate asynchronously.
For example: Slack and email use threading to group together a conversation around a particular subject.
As an enterprise platform, our customers have more complex jobs to be done around a conversation. This can involve additional participants being added to collaborate asynchronously, managers providing feedback on the way a conversation was handled, searching and filtering across all conversations to find trends, and more. Due to the nature of the Salesforce platform, utilizing a threaded UI for conversational messaging can provide a solid foundation for enabling these jobs.
Most short-term, casual, and social interactions are displayed using a chat bubble. That makes this pattern great for peer-to-peer applications.
Think of text messages and Social Media direct messages. While there are newer patterns in the industry around "replying to" a previous message within a chat bubble, it is not ideal for more elaborate collaboration. Often, the conversation flow is interrupted and a duplication of a previous message is displayed in order to provide context for the user when "replying to" another message. In short, a chat bubble is not ideal for conversations that might require collaboration.
Chat bubbles can be a great solution for a customer app, while a threaded UI is better suited to handle conversations on the Salesforce user side.