One of many foreign residents' biggest gripes about Japan is the requirement that they must pay into the Japanese pension system for as long as they work here, even though they won't stay long enough to receive any benefits. Permanent residency can help to side-step the issue without obliging somebody to work here for the 25-year minimum needed to collect a pension later.
The "karakikan" system, which is applied to permanent residents as well as Japanese citizens, allows for time spent abroad to be included in the 25-year requirement for receiving a pension, although time worked abroad is not counted when calculating the amount of benefits.
In theory, then, a foreign resident who pays into the Japanese pension system for 10 years, becomes a permanent resident, and then works overseas for the next 15 years while returning to Japan only to renew their re-entry permits will receive a pension from Japan.