This is a common misconception, but you do not have to pre-order the games to get Munchlax, nor do you need to get them from the same retailer. The official site says this:
You can receive a Munchlax that will evolve into Pulverizing Snorlax with an early purchase of Pokémon Sun or Pokémon Moon.
Those who purchase Pokémon Sun or Pokémon Moon by Wednesday, January 11, 2017, are eligible to receive an early purchase bonus via their Internet connection—a Munchlax that evolves into Pulverizing Snorlax!
To get Munchlax you simply have to purchase the game before January 11 of next year. It is received the same way as XY's HA Torchic and ORAS' Shiny Beldum event were. It is NOT a pre-order bonus.
So you're good, there should be no problem getting your Munchlax.