If I say match a b, without the concept of a line you would be unable to even work out whether a comes immediately before a space which is immediately before b with nothing else in between. Lines are indispensible for determining sequence. Whether a pattern is a b or ^b, the tool necessarily must determine what, if anything, is to the left of b. The dev took a shortcut and skipped the effort of analysing vertical significance between tokens. The pdftotext tool proves that text lines can be determined from a searchable PDF.
In any case, docs that lie or omit something important are always a bug. Man page says: “pdfgrep tries to be mostly compatible with GNU grep with some PDF-specific distinctions and additional options. Most notably, -n prints page instead of line numbers.” No mention of changing the meaning of ^ and $.