Hello Igor,
The documentation seemed quite vague to me. After thinking about it, I can see the clock free running being expected behavior. When stalling is disabled, the clock free runs until a transmit command word is written indicating that the transfer should end.
However, the issue with the last bit of the last word not being sampled with stalling enabled seems to be an actual issue with the LPSPI IP according to the link I included in my original post.