I think the point about the "podium" is a very good one. Here's a Street View photo right out the front of the apartment building I where I used to live in Gotanda -- a medium-density neighborhood of Tokyo. It felt like a "cozy" sort of area, as Davis Square does to me -- it's not in the middle of the hustle & bustle usually associated with Tokyo, and mostly empty of car traffic because it's an 5-minute walk from a subway stop and not on any major streets.
The main thing you'll notice is a mix of heights, from a couple of 2-story restaurant buildings, a couple of 4-6 story apartment buildings, the 8-story building I actually lived in, and also a 24-story condo tower. You don't even notice the 24-story tower in this photo (or when walking around the neighborhood) because it fits in with the vibe of the rest of the neighborhood. You'd have to actually look up to notice how tall it is, but in the normal course of a day that's not something you actually *do*.
What kept it feeling "cozy" for me was the pedestrian-and-cyclist friendliness of the area, and the diversity of street-level shops even on the ground level of all the apartment & condo buildings. There's 6 restaurants in this image, two barber shops, a hotel, a convenience store, a music club, a snacks & tobacco shop, a newsstand, two bars, and even a Domino's Pizza right behind the viewer (as well as a surface parking lot and a row of 8-or-so vending machines.).
Yes, it's more dense than Davis Square is, but my ideal vision for Davis Square would be exactly this sort of mix of the existing 1-4 story buildings, some taller 4-8 story buildings, and yes, a few (but not more than 2 or 3) tall condo / apartment towers, all with ground-level retail that's thriving and a minimum of car traffic. But from the standpoint of a tower building itself, I care a lot more about the looks & amenities (and pedestrian / sidewalk experience) offered on the first couple floors than what it looks like on floors 6-and-above.