My Portland Head #3262 is printed in black with the 5500 below the line not colored at all - but indented into the casting.

I don't believe I've ever seen what you describe.

I don't know what would be served by tracing over the "5500" with a black marker pen.

Is the "5500" indented into the flag? Or is it smooth with the 5500 inked onto a smooth surface?

I'm sure it's not a variation.

A photo would be great if you have the ability to take a close-up of the flag area.

If you don't have a scanner, send the photo to me. Email me by clicking on the envelope icon above.