I'm not an expert on PDFs but I suspect the text to page position hints are a little off, so it's highlight what it thinks is the letter, but it's actually somewhere to the side of that. I've experienced these kinds of highlight errors in other mundane PDFs before, so I don't think it's anything other than annoying.
A second source for highlight errors could have been capitalization, but this document doesn't appear to use lower case letters in its cyphered text. (On a side note, all the lower case letters you've used in the encrypted column should actually be upper case. However, case insensitive searches hide this error.)
This is bizarre. My first thoughts is that the document has been put through some obfuscating software, to remap the font to different characters. This would serve as a simple substitution cypher on the plain text, while keeping the document human readable. Doing this would serve to stop copying and pasting text from the document, and also stop searching from insider the viewer and web-search indexers.
From some quick looking I found normally non-printing character \u001f maps to a capital I, and \u0019 maps to a capital C. Those aren't ROT-17, even on an ASCII table. I think that some characters happened to be ROT-17 is an interesting coincidence.
One thing I do wonder about is what other PDF documents are out there that obfuscated like this, and are being overlooked because they're unsearchable.
Even if the plan turns out to be a fantasy or failure, that doesn't automatically make other matters raised by Q fantasies.
Someone versed in presidential transfer protocols would have to answer whether or not it is damning.
I suspect whoever did the redaction also did the scrambling too (probably a checkbox in the redaction software).
From my brief skimming of the document it details what the GSA is expected to supply to the candidate pre-election, and after the election if they win. Nothing I'd expect to find something nefarious in. Some buildings, names, departments and IT details have been redacted One redaction I do find odd is the redaction of the eligible candidate's signature and printed name (I don't know if this is standard procedure or not).