How do you avoid glue squeeze-out showing between light and dark woods?

Blue painter's tape is the trick you're missing. Put a strip on the show faces of the maple right up against the joint line before you glue, then glue and clamp as normal. Any squeeze-out ends up on the tape, you peel it off an hour or two later and the wood underneath is clean. I've done this on every light-wood-and-dark-wood glue-up since I ruined a maple-and-wenge cutting board the same way you're describing. The tape line also gives you a visual guide for how far the glue traveled, which is handy when you're checking your clamps are tight enough. On the washcoat question, a thin cut of shellac on the mating faces technically works but most people will tell you not to seal a glue joint, and I'm in that camp. The tape does the same job with zero risk to the bond. Another option for the walnut side specifically is tinting your glue with fine walnut sanding dust. It comes out dark so any squeeze-out into the walnut just disappears. Don't tint the whole batch though, do the maple joint with clean glue and the walnut joint with tinted. For the box you already made, keep scraping with a card scraper held at a low angle rather than sanding. Sanding rounds over the corner and can smear glue further into the maple pores. A sharp scraper with a light touch gets the last ghost out better than anything. Some folks also pop the leftover film with a warm damp cloth after scraping, which softens dried PVA enough to lift the rest.

For finish, skip anything oil based. Tung oil, danish oil, boiled linseed, all of them will amber up that maple within a year and your contrast goes soft. Water based polyurethane or water based lacquer stays water clear and won't yellow. A couple coats of water based poly, sanding lightly between, keeps the curl in the maple popping and the walnut staying that deep chocolate brown.

And yes, dry fit everything twice. Clamps staged, cauls cut, tape applied, before any glue bottle gets opened.

Pretty new to all this so take it with a grain of salt, but I hit the same ghost line problem making picture frames with maple and purpleheart. What saved mine was a tiny chamfer along the seam with a file after the glue cured. It reads as an intentional shadow line instead of a mistake, and it hides the last bit of haze completly. Might be an option on the box edges too since they're crisp corners anyway.

One thing I'm wondering about though, if the glue gets tinted with dark dust, wouldn't that stain the pale wood worse than clear glue if any soaks into the grain? Maybe I've got that backwards, but it's the thing that scares me off tinting.

I'd push back on the tinted glue suggestion. On this build every glue line touches both woods, since the maple sits between the walnut, so there's no such thing as a walnut-only joint. Tint that batch dark and the moment it squeezes out you've got a black line bleeding into the maple pores, which is way harder to scrape out than pale glue. I tried the dust trick once on a cherry and maple panel and the dark squeeze-out on the light side looked worse than the original problem. Clean glue on everything plus careful clamping pressure has always served me better.

On mine I left the maple a hair proud of the walnut, maybe a card's thickness, then planed it flush after the glue cured a couple days. Any squeeze-out rides right off with the shavings instead of getting sanded into the pale wood. Did that on a little ash and walnut keepsake box and the seam came out dead clean. Doesn't help the box you've alredy got, but for the two gift ones it might save you the scraping session entirely. Also second the dry fit advice, I tap two brads into the waste area of my cauls as registration pins so nothing slides when the clamps go on.

Update: tried the tape trick on the second box and it worked exactly like you said. Squeeze-out peeled right off with the tape, seam is clean even in raking light. Also left the maple a hair proud like the other poster mentioned and it planed down sweet. Glue-up stress is basically gone for the last two.