So strange enough that route made no sense (it made a Y). What options did you pick? Switched to the train and it said 36 minutes. Switched back to car and it was 35 minutes (18.5km) and the route had corrected itself. You did something wrong. I lived in Tokyo and the routine in the link you shared is not correct.

I made a multi-point route from Ikebukuro to.... iidabashi, then akihabara, then roppongi area, then down to shinagawa. It was mainly to get the 15 mile requirement while driving through downtown areas.

Or half an hour with public transport (your route).

So it's a half an hour for this start and end point, but that's mainly because they're both on the border of the "city center" (Yamanote line).

I live just outside the center (to the north, Ouji-Kamiya), and my workplace is just outside the city center (to the south, Naka-meguro), and it takes me about an hour door-to-door to cut across the city (50 minutes station to station), with 2 transits.

This is probably the longest possible way to cut across the city in public transportation, but I think you can expect 45 minutes to cut across in general, given transits.

The other problem is that the center is less than 15 miles in diameter, so a bit hard to get the same "feel" as LA for the comparison.