Management have no cross cultural training or, in many cases, no management training at all. I have seen instances of new kids fresh out of school promoted to low level managerial roles because middle management sees them as easier to deal with (no experience means no backtalk to middle management for questionable choices). Middle managers generally don't know or can't understand what their staff are working on and focus on verifying that everyone is at their desk from 9am to at least 5:30pm.
If you're on the business side, you may have to be at your desk from 8:30am to 9pm instead of 9am to 5:30pm. You don't have to work, but you must be in the office. This is common to many large Japanese companies.
If you have any sort of ambition you will not want to work forever in a place where your actual contributions do not affect your compensation. Team building aside, this policy favors the lazy and leads to low levels of workmanship in many instances.
No one can argue with decisions made by the CEO. All managers fear to displease him. Many rules are obviously passed down from the CEO with no oversight - for example - we didn't have flex time for many years because the CEO heard (incorrectly, they actually banned remote working) that Yahoo banned flex time due to staff goldbricking. For another anecdote, I was told by colleagues in a branch office that they were instructed to remove all personal items, monitors, etc. from their desks before the CEO visited their branch because he prefers to see clear desks. I suspect CEO related problems are the root of many of Rakuten's other problems.
I have the strong impression that HR is attempting to gradually roll back secondary benefits in order to cut costs (cost cutting necessitated presumably by unfortunate business decisions made by the CEO). For example, during my five years at the company they have provided a special lunch for vegetarians at the company (which is a big plus in Japan). When I joined they allowed vegetarians to sign up to receive one of two lunchboxes each day with a vegetarian dish. After four years they changed from the lunchboxes to having the food dished out onto a tray (no problem here). Then after a couple months they decreased the number of selections to one (no real problem yet, but the erosion has begun). Then, they banned all non-Indian employees from registering to eat vegetarian food (there are no enforced laws against discrimination in Japan). After another month or two they then decided to decrease the amount of total food available so that of the 600 or so vegetarians at the company, there is only food for 1/2 - 2/3 of them. Now a long line forms for the vegetarian food earlier in the lunch hour. You must show up early to wait lest you be one of the unfortunate ones who lose their chance to get catered lunch that day.
The above case only applies to vegetarians, but you may want to consider if it's a good idea to work for a company that tempts you in with advertised benefits and then slowly shaves them away as much as they can without causing too many people to quit. Also, do you want to work for a company which behaves this way when doling out benefits, bonuses, and raises? (HR must approve all raises even if your own boss requests one)
The salary you have when you join will be very similar to the one you have when you quit (not much chance for any big raises even if you gain more experience or responsibility).
No vegan food - if you're vegan you'll be cooking for yourself.