why do some submissions have the CRC calculated for the main data, when they require the headered romThis seems to be a common point of confusion. There are two different things you can calculate a hash for: a ROM image, and a file. Sometimes they're the same thing (headerless SNES ROM for example). Often times they aren't (iNES ROM, SMD format Genesis ROM, etc.).
There is an advantage to using a ROM hash instead of a file hash: it will tell you if you have the right ROM, even if it's in the wrong format or has a corrupt header. We recently had a few submissions to "correct" hashes for SNES hacks. Different people got different file hashes from different copies of the same valid ROM, due to differences in the SMC header. This is why emulators only deal with and provide ROM hashes.
You can specify either a ROM or a file hash for a submission. Both would be preferable, but at the very least, you should specify whether the hash is calculated based on the ROM or the file.
Now let me shamelessly plug this little doohickey: ROM Hasher. It calculates the preferred hashes and presents them to you in a ready-to-copy-and-paste format specifically for RHDN submissions. It's also good for verifying ROMs. It checks them against the No-Intro database, and provides details about the format, headers, etc.