How to fix Cover Flow size behaviour?
The preference is stored in the FlowViewHeight key. Something like defaults write com.apple.finder FlowViewHeight -int 180 only changes it temporarily, but you could run the command every minute by running EDITOR=nano crontab -e and adding a line like this:

* * * * * defaults write com.apple.finder FlowViewHeight -int 180


Or just make the default size of Finder windows bigger.