For instance,
Does setting LoRom/HiRom/FastRom actually affect system operation?
If any of those bytes affect actual system operation, please inform me. All these years I just thought they were for info purpose and not actually affecting the system operation.
The internal header was used by Nintendo and by emulators, but not by the SNES itself. Most of the properties it describes are either a function of the specific PCB used or values written to control registers by the CPU.
So a cart that states that it's LoRom or HiRom doesn't mean anything. A 'LoRom' cart can wire its ROM to SNES A15, for instance. Learning more about memory mapping goes to show how little the words LoRom or HiRom can mean, especially in mixed mapping situations.
The question is somewhat vague -- Subject says "SNES ROM Header", which I can interpret in two ways. Are we talking about file headers, for example the data in the 512-byte SMC header, or are we talking about the "cartridge header" that ends up at $FFB0 to $FFDF?
If we're talking about the cartridge header -- they are supposed to be correct, given that these are what Nintendo requires to be accurate per their own submission guidelines (see developer manual page 1-2-8 onward, 1-2-14 will also interest you). However romhackers, independent homebrew folks, amongst other things/people often muck these up (or forget about them), which causes frustrating situations for emulator authors. But generally speaking you're supposed to trust what's in the cartridge header -- it's the "one-off" situations that require weird heuristics and other logic. I'm sure byuu can talk about this extensively, if there isn't a blog post by him about it already.
Regarding actual console operation -- no, these have no effect. All the "mapping" is done at the hardware level, as lidnariq states, barring extension chips that might let you change a memory map/model in real-time.
Thank you for being accurate Koitsu.
For the record, I am referring to the physical Cartridge ROM Header, and the question has been answered. Thanks guys.
Not having worked for a Super NES licensee (I didn't graduate until the GameCube era was already well underway), I don't have the official developer manual. I assume the internal header was used as instructions to Nintendo's manufacturing plant to choose which board to use; is that roughly correct?
Sort of. What got manufactured cart-wise was what you included on written paper. It's just that "all the things" (cartridge header, paper forms, etc.) are supposed to match up. Check your PM as well.