Different selectorates, different priorities. MPs who voted for the final two to be on the ballot had more established personal and political relationships with other candidates and saw her as an inexperienced MP with a few strange ideas about organising the Cabinet who was obsessed with culture war bullshit. The Conservative Party membership that didn't get to see her on the ballot were impressed with her debate performances and loved the culture war bullshit.

(tbh I didn't see much indication she was the 'most popular', but there were definitely plenty of members of the party receptive to her message, doubtless including many of those most likely to espouse racist sentiments)

Most popular with the membership but too radical for the MPs. It’s the same as Corbyn with Labour members and MPs.