depends on your tolerance for repeatedly taking the liner in and out of the boot.
most athletes with that set up leave the liner out and string the pull loops through the power strap when transporting them so they do not forget the liner. you have to be careful not to lose your boot boards during transport. screwing in the boot board is standard fare for FIS athletes for height consideration and loss prevention.
good reasons to leave the liner out:
liner dries better out of boot
less wear and tear on the liner the fewer times that it goes in and out of the shell
good reasons to put the liner back in:
you have a lot of spare time on your hands
you are a virgo and cannot stand to have things out of place or order
OCD, anal retentive, etc
you are a major cluster%$k and tend to lose or forget things like your liners, your boot boards, your footbeds, and your wallet/purse