While I was quick to make use of the startpage.com “add search engine” button there isn’t really such a friendly method to add a search engine to thunderbird.
Long(ish) story short thunderbird and firefox use very similar methods to store your profile information, the startpage.com configuration for firefox is stored in
/home/<your user name>/.mozilla/firefox/<a random string>.default/searchplugins
I noticed one article talked about adding google as a custom search engine and mentioned creating a searchplugins directory in your thunderbird profile
/home/<your user name>/.thunderbird/<a random string>.default/searchplugins
So I copied the file startpage-https—uk.xml from the firefox profile into the thunderbird profile.
It was just then a matter of searching for something in thunderbird using the current default, clicking the searchpage icon on the left and then setting it as the default (heart icon at the bottom left)