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Keep in mind that the pdfiototext program is just a proof of concept/example. If you need text output there are far better options available...
In this case, the spaces are placed between fragments in the content stream. This particular file does a lot of kerning and pdfiototext is not smart enough to merge adjacent fragments.
Trying to understand how to pdfiototext.c works. The code seem to output too many extra unnecessary spaces for this PDF.
weird_spaces.pdf
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