If only the 'boot' is a 16-bit component which runs before Windows 3.11 it definitively is a DOS program rather than a Windows program and if you want to change color output it means that you need to manipulate a 16-bit DOS-Box. That probably can be done by using escape sequences in the output statements sent to terminal (screen).
Yea the boot part is just a boot loader that lets you enter a password and it runs before windows so yes, it's a DOS program. How do i use escape sequence if i may ask.