We have done online check in for awhile and the latest version seems to work pretty good for us. However, if we make any requests for the room including traveling with labels, we never ever fill out the portion on the online check-in regarding view requests. So far no problems, MBs work at resort* and park, and for CC charges. *Note until you have keyed your room with your MBs, the MBs will not open doors and pool gates at the resort. At the Poly they will issue you a temporary card to access the pool while waiting for your room to be ready.
If you are uncomfortable with it don't do it. I prefer to skip the line at check in when I can.