It is pretty irritating when that happens.
You could try this switch Menu> Preferences> Configuration Manager
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For example, Sylpheed, the email client, re-opens in the last position and dimensions. Other applications might have a switch to turn off/on previous setting.
I'm not familiar with Thunderbird, but I think the developers might be pretty proud and want it to be 'front and center', every time it is launched, unless of course there is a switch inside Thunderbird that 'remembers' last placement.