Part of it is Lua runtime, which uses a random hashing of tables so the performance of each launch can vary up to 10%. This is done for security purposes to try to prevent people hacking games, as table contents will be in different places each launch. I don't know enough to argue whether or not it is needed on am embedded device. But, as a test, Dave tried removing this feature and indeed the performance penalty went away.
Over on Discord there have been more discoveries about the other performance differences, but I need to investigate so it's too early to talk about those. You can read it there for now.