You don't always have a choice - because there are no or few daycare facilities available anyway, and you may not live close to your parents either.
As you mentioned, don't generalize to everywhere in Japan. I can tell you even in Kansai it's far from ideal and the daycare facilities are completely full and you need to reserve more than a year in advance to even have a chance to get your kid in.
This was last year. The situation is very much still problematic, even in cities.