The whole ROM-Patcher step is about creating a header.bin file for NO BAN NO SKY.
Rom-Patcher should even let you select which chip ID the private header belongs to. It has to be injected into the ROM before it can be extracted. Otherwise you're just exporting the ROM's general/blank header. Which is why you'll need a copy of a ROM that you can trash later.
What's worse is trying to find out which Chip ID belongs to a private header if you didn't dump the ROM or header from GW menu. Especially for those that used the Powersaves method for getting private header.
And trust me, I know I'm doing it wrong. But this method was the only way I got it work. Powersaves>private header>ROM-Patcher>export header to header.bin>NoBanNoSky>spam template
Perhaps using ROM-Patcher to change Chip ID per game template will work? I have no idea. Didn't try it. All I know is that I had to retreive a private header using Powersaves and guess what Chip ID it belong to by using the template for finding the Chip ID line.
Once I knew I had a C2 header, then I exported the header through Rom-Patcher to use with NoBanNoSky.
The key difference in NoBanNoSky is to apply to all of template instead of to a single rom template. This allows you to skip connecting a ROM file. So double-click template file, green, double-click header.bin, green, then apply to all of template.
I'm not quite sure why others have been able to modify the Chip ID to the template so the header will work.
Some say SAK works, others say NBNS. Personally, I had to make sure my private header was a C2 to begin with before I even injected it into my template.
So maybe certain headers work with any chip while others are specific.
What I do know is that after I used GW to dump my ROM/Header my C2 header had a special unknown byte of 0x08 in it, but even without it, it worked.