Keep in mind that the person who answered the phone might have been a younger employee at immigration, unaware of recent changes or even old policies. That's the main reason they asked someone else (older, more experienced).
Oh, and those years of "significant contribution to J society" are all nebulous (see the examples on the immigration guide book page), but essentially I wouldn't count on the experience you've had so far to count for SIGNIFICANT contributions. That makes you a regular foreigner, and you should probably heed Majestic's info.
Keep in mind that just filing for PR costs nothing. Only when you get it do you have to pay (8000 yen, if memory serves). And, you can file at any time, that is, when you currently have a valid visa. You shouldn't wait until it expires to apply.