Upload-based tools create a trust decision
An upload-based PDF tool may need the file to render pages, convert formats, compress assets, run OCR, or store a project. That is not automatically bad, but it does mean the user is trusting another system with the document.
For sensitive paperwork, users should ask whether the task actually needs a server. If the goal is only to remove pages, reorder pages, rotate a page, or combine files, browser processing is often enough.