I'm doing a rebase and I want to keep always the changes made in the latest commit to avoid having to resolve the conflicts manually.
Unfortunately, most likely you can't.
When you have multiple commits that are conflicting during a rebase, each commit is replayed one by one. From the point of view of conflicts at each commit, the changes in the last commit don't exist yet, so it wouldn't be possible to automate choosing the final version of that file.
So what can you do? There are some options that might work for you:
Also, as chepner mentioned in a comment, you may be able to use rerere
to assist with resolving similar conflicts on a per commit basis during your rebase.