What is actually on the transcript
Every course and grade from ninth grade onwards, in nearly all US high schools, along with the cumulative GPA those grades feed. That is the document your counselor sends, and it is not editable.
What varies is how it is used. Some large public university systems recalculate GPA from tenth and eleventh grade only, and some recalculate using core academic subjects alone. Others read the transcript as sent. There is no single rule, which is why "do they count" has a longer answer than it should.