Without a photo, it's hard to tell. Is the secondary door more 'insignificant' in some way now that you have painted the main door? I wouldn't think that 2" in size would matter all that much and would perhaps make your real front door stand out even more, which is your goal.

When you ask about housing color, are you talking about for the spots on the corners? Are you using black anywhere else? What is your window trim color? I'd probably use white. It would stand out less.

Recommendations for outside lighting is that those lights near the door be 1/3 to 1/4 the size of the door...or about 21" - 28" tall for a 7' door. I usually go at least 1/4, but have noticed that way too often we (or builders) use lighting that cheapens the look by being too small. Here's a link to one article on the recommended size. Exterior lighting size guide

Since there's some confusion about which is the front door (and I think your painting it red should help with that), what if you put a different style at the secondary door? I'm thinking put the regular lighting at the front, then an inconspicuous light (like a boxy or sleek style that doesn't scream it's a light until it's lit.) They can almost look like part of the door trim or siding until lit. Or if there's a porch, just use a ceiling pot light at the secondary door.