The short (and unsatisfying) answer is that back in early 2013 when I first added the Lua runtime to the project we didn't even have a filesystem yet so I took out package because there was no way to load code at runtime. I added import as a replacement for require and the compiler generated flat pdx files, not folders. After adding external flash and a filesystem I never went back and reevaluated that because import was working fine, and also because we'd seen a number of game devs build huge Lua frameworks that ran okay in the simulator but tanked the device. Lua's package feature always felt to me like a desktop thing, not appropriate for an embedded platform.
Yes, we need to make it clearer that we support the core Lua language but not the package ecosystem. I've got that filed, will take care of it soon.