I only want one of my accounts to make the mail indicator go blue when I get a new message, but I don't want it monitoring the second account I also have in Thunderbird. Possible?
I don't know any settings to customize the Message Indicator behaviour. By the way, as a workaround, you could disable the "Check for new messages on startup" and the "Check new messages every..." in Thunderbird account settings for the second account you don't want the icon to get blue.
To access these two options,
If you do this, just remember sometimes to manually download messages for the second account.