No, a cheap apartment in Japan will not compare to the comfort of your parent's familiar and comfortable house - but neither will a cheap apartment (for the same income equivalent cost) in your home country.
What people need to know is that you are STILL going to have to put forth the same effort and do the same type of boring "work" as you would have back wherever you came from to get by. Your standard of living isn't going to shoot up if you are still making the same kind of income, and it will go down if you are making less.
I think another problem is people also forget that Tokyo and big urban areas are more expensive than their hometowns too, or they don't appreciate HOW much more expensive it is. I've heard people complain about being 'ripped off' on their rent prices for their small apartments, which sounded genuine until you realise they're comparing it to what they payed on student accommodation in a suburb in Stockton or something and not to the actual local prices in Japan or even big capital city prices.