It's not that this place is so bad; it's the opportunity you will be missing that will cost you.
(This review is based on my personal experience in a particular group. I don't think every group is the same. So ask, observe, and do your research about a group.)
First of all, this place is called a "research" lab, but it's barely one. Some people, when they decide to forget about financial gains (will come back to this later) and join a research lab, want to publish papers and build up an academic profile. If you are one of those people, think twice about joining this place, especially some groups. Look at if any of the recent departures from the group went to a place you'd like to be. If the odds is against you, there is probably a good reason there. You may be different, but you will still be constrained by the lab. You will probably get much less "research" and much more "development" than you thought. "Freedom of research" is more often just used to entice you to join; after you join, you will likely be assigned something your manager tell you "very critical" for the company and you have to do it. For those who really wants to do academic research, it's much better to find a postdoc position with a great mentor. I know, you will sacrifice a little financially, but the long term gain will be worthwhile. Plus, you are not going up too much anyway.
Secondly, your direct manager's power is pervasive and democracy is non-existent. Of course the org is flat and on top of your manager there is Roger (president, who is kind and approachable, by the way). What this means is that, managers have no chance to move up in the company, because they can't replace Roger. When you get no chance to go up in a company, what would you do? You think about next opportunity, and you don't think about taking a long-term view in managing and helping your reports. Some manager chose to use everything they could to get things for themselves in preparation for a future job jump, and some times this is at the expense of what could help researchers. When your manager takes a very short-term view to maximize his gain, that's bad news for you. What makes it worse is, your manager decides everything, literally everything, from what you should work on on a weekly basis, what intern you may get in the summer (if you get one), what's your performance review and bonus, and who you should put on your paper (Of course, manager gets to be on almost every paper, regardless of how little he does for that paper.) This kind of massive power on a manager can easily produce dictators. In the meetings, generally people are obedient towards the manager, rather than actively voicing their opinions. It's sad.
Now let's come to compensation. Japanese companies generally don't believe in giving out equity (stocks) to employees. It's a fact that, in the bay area, you can't live on wages alone. Houses can easily go 1.x million if you want to be in a reasonable area (with good elementary schools and close to where you work). This is a very realistic problem if you want to have a life here. Don't forget that you will not get what you are offered - it's taxed much higher than when you were at school so you will get about close to half of that amount. Think about how long you will be able to get your down payment for a house and pay back the debt. Compare that with upstart American companies. It's very easy to find such information from friends or online. Realistically think about your livelihood and think if it's going to be worthwhile to make half of what you could make for a few papers that you may or may not get to publish.
Some people chose to join this place to get a green card because NEC applies for it for you right after you start. This is totally unnecessary. With your papers and PhD degree, you will get an EB1 green card almost anywhere you go in a few months. The cost totally outweigh the gain.
And finally, you want to be working in a place that you are proud of. Consider if this is going to be that place. If you are the kind of people who want to get a "wow!" when you tell people where you work, you'll be disappointed if you join this place.