Yes.. the safety systems (intrusion mats, beams, etc..) can be disabled and vehicles can be moved around manually.
It's actually how/when most damage to ride systems occurs. Normally the failsafes of the operation prevent vehicles and show objects from getting anywhere near each other. Vehicles hitting each other and show doors closing on vehicles and such tend to happen in the manual mode.
Each ride system is a little different, so just how much can be moved or how it is moved varies, but people walking around inside of the ride (but outside the ride envelope) is pretty common too.