It really depends on your needs and what and how you need to markup/annotate.
I like that Files gives me basic markup tools. When a collaborator needed the names taken out of a student work sample I could do that right away just on Files.
You can add handwritten (or Pencil-written) annotations, etc easily enough in Files.
But for full featured markup and choices about export locations and formats I’d use PDF Expert. PDF Expert has come in handy in many, many PDF conversion and markup situations for me. I also use PDF Expert to give me a better reading experience for long documents that I keep in a synced folder.
Notability also has good markup features. It’s just that for my workflow, I use Notability more as a storage/journal app and not for annotation and sharing.