Modern PDFs essentially describe the result of a 19th century-style metal-based typesetting process. When typesetting Arabic, Unicode is used as a glyph list, rather than a character list. The glyphs are used as indexes into a huge font book.
By interpreting the Unicode standard as a look-up for glyph indexes, Unicode is abused as if it were a huge font book. This confuses multi-lingual encoding with computer typography. Unicode is set up as a catalogue of nominal characters, independent and irrespective of the (computer) typographical consequences.
An underlying cause for this error is the idea that there can be such a thing as a Character-Glyph model. However, in the real world there is no connection between abstract characters and the glyphs used to represent them.
Increasingly font designers are discovering the enormous conceptual freedom one gets without any Character-Glyph constraint. But Adobe still uses the Unicode standard to extract the nominal character values from the font glyph numbers used to represent them. That is why more advanced Arabic fonts that do not use the Unicode Presentation Blocks produce gibberish when text is extracted from the PDF.
Future versions of PDF are planned to embed Unicode as text in addition to the font information, which would resolve this issue.
Part of the problem is that Unicode’s Arabic Presentation Blocks are officially deprecated by the Unicode Consortium. Their inclusion was at the time – late 1980’s - a technical compromise to allow the ISO 10646 to join Unicode. As such the compromise was incomplete, as only 400 out of originally 4000 requested Arabic ligatures we allowed to remain in the Unicode Standard. Ironically, all the printed examples in the Unicode standard were designed by Thomas Milo based on computer-generated synthesis of the underlying letter block fusions of traditional Arabic "Script Grammar". This was done using DecoType’s famous ACE technology, that eventually became the working model for Microsoft’s True Type Open, the precursor of today's OpenType.
Arabic Presentation Forms should never be encoded, such a practice amounts to reverting to Font Pages, whose very proliferation caused the development of a more intelligent alternative: Unicode.