I have the same issue. Some email of a same subjet are sent to differents email addresses. These have to become new conversations.
Conversations should be separated by object (as it’s done today) and email addresses ! Or at least give us the option.
Here is a probleme caused by the current behavior : when I want to answer with the shortcut (ctrl+R) to one specific email (with X and Y email addresses) opened in the conversation, the answer is sent to the people in the last message of the conversation
You can reply to any single message in the conversation. Just open the conversation and select the message you want to reply to. Either right-click in that message and choose Reply, or click on the reply icon below the time.