Mikita, your home prices astonish me. What gets you a whole house where you are isn't even a 20% down payment In the CA Bay Area. Wow.
Here's another Zillow twist: per b42's suggestion, I claimed our primary and our rentals and updated the information. It had no significant impact on the Zestimate. It seems the shortcomings are primarily around the finishes. Have stone floors? Unless they're slate, the closest option is "Tile". Custom cabinetry? No box to check. Paver driveway vs. concrete? No box. Is your house in the more sought-after school district than the comps? No way to change that. You can only eliminate three of the ten comps, even if more are not true comps.
The same was true of the rentals. One in particular was way off. It has a fancy outdoor kitchen, sun shades, high-end retractable awnings, expensive air and water filtration systems. It also has a true three car garage instead of two and a golf cart garage. All of those things add value to a home in this market, but Zillow doesn't recognize these features.
Again, none if that matters if I'm not selling. The biggest takeaway I've seen from this discussion is that listing a house for way over the Zestimate will impact traffic, which is an angle I hadn't considered. In that case, is try contacting Zillow directly.* I'd also made sure my photos were beautiful and that the description mention all the upgrades Zillow doesn't see.
*I have done so in the past and always gotten a response. For a while, someone was running a scam using listing photos of homes for sale and recently sold as homes for rent. It happened once to a house we'd recently sold. Another time, a house that was owned by a pro ballplayer was listed for sale with one set of information and for rent with completely different contact info. I knew the property (alas, not the ballplayer) so I knew the rental ad was a scam. Zillow pulled it less than 24 hours after responding to my email and asking for more details.
Oh, well. No big deal in the grand scheme of life. It's an imperfect tool, but it's better that what we had before.