There’s a couple of reasons that come to mind.

• Bragging rights
• Spare parts
• LED lit PLA MakerBot
• Removing the fiddly bits

I really like Webca’s faithfulness to the MakerBot Cupcake design.  However, once you are free of the constraints of trying to build a 3D object out of lasercut pieces – the possibilities are endless.  The small lasercut assembled bits underneath the X stage and the entirety of the Y stage could probably be printed up as a single chunk of plastic.  This would reduce the steps, materials, and dexterity required to assemble some of the fiddly bits of a MakerBot.