If you look again at the manuscripts of the cancelled chapters of 'Persuasion', you will see that there are indeed examples of underlining used for emphasis among all the editorial crossing outs. There are three instances on page three:-

"... but that will all come out in the right place."

"I thought we were not mistaken."

"...evidently beginning to deny his mistress,..."

There are further examples on pages 5 and 6, and perhaps more later on (page 6 was as far as I got).

Like you, I initially thought that what I was seeing was all editorial deletions. I found it easiest to pick up the underlining for emphasis by skimming through the typescript on the left, then checking across to the manuscript.