SPI programming flash chip(s) - connecting HOLD and WP pins
The full paragraph:


  You may also need to connect pins 1 and 9 (tie to 3.3V supply). These are HOLD# and WP#.
  On some systems they are held high, if the flash chip is attached to the board.
  If you're flashing a chip that isn't connected to a board, you'll almost certainly
  have to connect them.


The guide is telling you that if you're programming a flash chip while it's on a board, the board likely ties HOLD# and WP# high to the 3.3V supply (likely through a resistor). If you put the clip on the flash chip, and provide 3.3V as instructed, the 3.3V rail on the board will be energized, pulling the HOLD# and WP# pins high.

If you're programming while the flash chip is NOT on a board, there's no path from the 3.3V supply to pull these pins high. Thus the guide is telling you to do so.

If you're programming outside of a board, I would recommend connecting a resistor, e.g. 10k ohms, between HOLD# and the 3.3V supply. Similarly for WP#.