Having used Clipper a few times, I think an easy way to make it less annoying is to just have more card readers. All the stations I've seen have so few you have to scan the entire platform to look for one.
Completely agree. Bad design to place card readers in non-obvious places. You should be basically unable to leave the station without running into one.
Or card readers next to the train doors. People usually spend a few minutes next to the doors before exiting -- there's no reason why they couldn't tag off then. The train would be smart enough to round up this tag location to the next stop.