I did my PhD at Titech (Suzukakedai).
The 3-year limit is not a hard limit. It is common to have an extension. It may also depend on the department. Most foreign students drop after 3 years due to a lack of funding.
Compared to the research culture in the UK/US, I think Japan is much better. Yes, you may be forced to overwork and sleep at the lab, but the guidance and supervision are good.
The only thing I hated was that COVID hit right before the graduation ceremony. All we had was an online ceremony.