Winning an election on one manifesto, being chosen by 100k members, and then ripping the manifesto up and trying to implement a set of completely different policies would strike most, I think, as not 100% legitimate even if it's legal.
And just to add that she campaigned with members on ripping up the manifesto.
https://www.britannica.com/topic/legitimacy
While I agree with you that it would be incorrect to call Truss' premiership illegitimate, I feel that uniqueuid's comment was using the term according to the above usage.
The larger issue is that the new Tories' procedure for producing candidates leads to a winner that has a large majority of parliament against her.
There is now a problematic mixture of parliamentary and Tory voter legitimization. That would be resolved by a true general election.