I think I understand where you're coming from.
The issue comes into play with the last "relative" reference InDesign makes as it addresses the file system. So yes, when you save the PDF for Document A in the "X" folder, it wants to place the PDF for Document B in the "X" folder too -- unless you tell it otherwise.
It's always dangerous to make assumptions. But one I'm going to make here is that you have multiple InDesign documents open, from multiple locations, at the same time. InDesign allows you to do this, of course, as a matter of efficiency. But that causes you complications when you're looking to shuffle content around multiple locations.
With my students, I generally deal with this problem because the program wants to store "Save As" InDesign files and PDFs in the same location where they last placed content into the document, rather than the folder containing the source InDesign document.
Unfortunately, this is how InDesign is, well, designed. I can offer three workflow/workarounds for you, none of which may be entirely palatable to you:
1) Open one InDesign file at a time, from within the InDesign File>Open... menu command. This gets you the "relative" reference to your document folder, but defeats the efficiency of working with multiple files at the same time.
2) Set up a separate "repository" folder for your PDFs, and if need be, distribute the contents back to the respective document folder(s) at the end of the day/week/production cycle. That results in extra work and the possibility that PDFs get mis-filed in the wrong folders.
3) First save your InDesign file, then create an InDesign Package using the File>Package... menu command. If you're using InDesign CC2015 or later, that lets you create a PDF with your latest settings while you create the InDesign Package. By first saving the InDesign file, you set the "relative" reference to the folder the InDesign document is in. But Packaging the file creates a sub-folder inside it which will contain a duplicate of the InDesign document, the PDF file and, if you don't uncheck the fonts and graphics check boxes, duplicates of those files used to generate the document as well. So this results in some redundancy which may or may not be acceptable to you.
Of course, you can also keep on doing what you are to place the PDFs in their respective document folder(s). I wish I had better answers for you, but I believe these options are as good as it gets.
Randy
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