Edit: The issue was resolved, so please ignore this message. Thanks u/artillect!
There was an issue where the parent comment was in a column on the left side and its children were all on the right, but I adjusted the CSS:
.entry-comment .children {
/* grid-area: children; */ /* disable or delete this */
display: flex;
flex-direction: column;
}
.entry-comment .comment-level--2:first-child {
margin-top: 3rem; /* Edit: If the child comment is long then the text will get cut off, so setting the margin and/or parent height conditionally could work*/
}