OK, here is a temporal file that adds that preference (file/preferences) to move the caret to position 0. Just replace the pde file from c:\program files (x86)\arduino...
I will build the full setup after testing adding line numbers and making the upload hex work, but I am not sure how long that will take.
Also, attached is a preliminary version of the line numbers, should they have some line or special coloring area? I am yet unsure how to handle bigger numbers, right now the "dynamic" offset is buggy but a smooth one will be a bit more resource intensive (calculating the length of the last line number when scrolling):
pde.jar (814 KB)
pde-line_numbers_experimental.zip (777 KB)