Not sure why. I used a voucher last time, didn't have any problems using it to pay for my stay at the hotel. (Hotel C-Stockholm).
The advantage of the vouchers is that they don't expire.

Stayed in 2 Preferred Hotels in Japan

Royal Park Hotel Iconic Shiodome
Sapporo Excel Hotel Tokyu

The Royal Park is a fantastic hotel. Location is also relatively good. Tokyo is a spread-out city so you can't be close to everything but this hotel is near a major station and in a good location for eg. Ginza & Odaiba.
They have an iPrefer hospitality desk in the lobby. I got a welcome drink in the room (full bottle of French wine) but there was no card with a message so I made a call to the reception to verify if it was indeed a welcome gift.
Asked for a late check-out but they charge a fee per hour and I didn't want to beg, bring up the status etc. Just worked for a few hours in the lobby.

Sapporo Excel Hotel Tokyu: Nada, nothing. No mention of status, no welcome drink, no upgrade
Individual hotels might give you something extra for your status but I have the impression that chain hotels only see their own status members in the system and don't really keep track of iPrefer.
The points do always post without problems. I'm not sure how this works but I think the hotels don't have to do anything for this. Points usually already post on check-in.