Yes. There is a way to do this using the config editor.

The source for this solution is a post by user billko at http://forums.mozillazine.org/viewtopic.php?f=30&t=1463325 however users of current Thunderbird version may get confused with the steps provided in that post (as I was) hence this Q&A. This will also be useful for Ubuntu+Thunderbird users who look for solution here.

• Open Thunderbird Mail


• Go to Edit > Preferences > Advanced


• Click on 'Config Editor' button


• Agree to the warning


• In the search box type account


• In the list of options displayed, look for the email addresses and identify the accountn vis-a-vis the servern vis-a-vis the mailbox, where n is a serial number in the order in which the account was created (see image below)


• Now edit value against the preference-name mail.accountmanager.accounts to reflect the sort order you want
  
  eg. in my case, I modified the original order account1,account2,account3 to account3,account1,account2


• Now also edit the value against the preference-name mail.accountmanager.defaultaccount to the first account in the sorted list as above
  
  eg. in my case, I set it to account3

Image: Thunderbird config editor - account sorting