I work for a construction design company, and marking up on PDFs is a very common task, so we use Bluebeam. I've found it's better just to have the agent call the MCP with python or edit the pdf directly, since (at least with Claude) there's no way to pipe data into the MCP directly; the agent has to output everything itself. For this reason alone I feel like command line tools are just the better way forward for most things.