EDIT: Got it working!!!
*hugs to Kirby!!!*
To clarify what I was doing wrong:
First you need to look at your original templateXXXX.txt file.
Then Use Sky Army Knife or ROM Patcher to load up the ROM and find the CTR-P-XXXX.
Go back to template and FIND the same CTR-P-XXXX.
Check the CHIP ID header (illustrated earlier) and see which chip it runs. Then try your private header that would work with said manufacturer.
So the needing x3 headers is relevant. You need one of each manufacturer to match them to the template.
Most important is finding the Macronix private header.
Or let's say you have a Pokemon ORAS private header. You could just use it on all Pokemon ORASXY games since they all use C2 (Macronix).
Or let's say you have Smash Bros. That's an AE (OKI semiconductor). So if the template has an AE in it, apply the Smash Bros header.
Same goes for 45 (SanDisk).
Luckily you can guess or match your Chip ID by simply referring to the template file itself. Find CTR-P-XXXX of the game you got your private header from, and chances are that's what type of chip manufacturer it is.
I was actually trying to force the whole Chip ID into each game on template through SAK. All I really needed to do was know my private headers and the manufacturer it matched.
So when I checked the template for my private header, I knew what manufacturer it had.
Then I just made a copy of the game ROM it came from (not an actual dump) and used ROM Patcher to inject the private header so I could export that header to mass apply with NO BAN NO SKY.
Then I deleted my ROM copy with injected header (since I didn't need it anymore after exporting the .bin file).
Went back to my private header list and repeated whole process or matched the games and just copied the private headers into the template without editing the Chip ID.
So leave the Chip IDs alone in template. Just use the template as a guide to find the Chip manufacturer and match your headers accordingly.
If you know which private header is the C2 (Macronix) you can just spam it through the whole template and then go back through and insert your individual headers matching the proper game.
I was trying to actually edit each individual Chip ID and had no idea what it was because I didn't reference the template file appropriately.