"I read that epoxy primer (spi) should be as close to the same color as the base for coverage. Do you think it's necessary to use two different colors of primer as well?"
Usually does not need to be the same color BUT about the same shade of gray to get better coverage. Certain transparent colors (metallics and pearls) require the same color & shade to spot match.
"Will a cheap spot sandblaster from harbor freight work on the small rust areas without ruining the panels?"
Should work well but don't get tempted into turning up the pressure to go faster. Turn it down and take your time. DO get a pro respirator, blasted sand is ground glass, nasty stuff.