With regards to programing 'clean up' as I like to call it, there are a few ways to do it. The easiest way is a the Hog, it let's me do separate timing for every function a light has. For example, I can snap a shutter shut with a fade time of 0s and then have the fixture move and change color over however many seconds I want. Make another cue that follows that the first cue and opens up shutter once the light is set. Another way to do it if I want to see movement but not color change is fade the fixture out on the 1st cue, follow it into the 2nd cue which snap changes the color but fades the movement and have that follow into another cue with a delay of .5s for the color change that fades the light back up or snaps it on again. Since the Hog is tracking, it only changes the values I change in a cue. So dispute following into the 3rd cue, the fade on the movement continues since I didn't change pan and/or tilt values on the third cue. I love tracking.
Now for a cue only type desk, programing something like that takes a little more thought. My first cue would be a shutter shut, this would follow into a movement and color change which then follows into a the shutter opening back up again. Now if I want the movement to be seen but the color change to not be seen, first cue would snap the shutter shut/fade the light, followed by a snap color change which follows into a movement and fade up the light cue at the same time. The only issue with this, however, is the light won't be to full until the movement is complete since I don't have as much control over timing. I can get around this by changing the dimmer curve on the fixture to make it fade up faster (75% is full instead of 100% for example), but then have to keep that in mind for the rest of the show then.
I can also do something like this on say a Magic 260 since it has fade times and speed times (which are really follow times). It would just take me a while since there is a lot of paging over I have to do on that desk.
Syncing stuff to live is a royal pain. Unless you are touring with the band, you just have no idea what they are going to to and when they are going to do it. Major tours a rehearsed for a month or more before they go out. They know what the band is going to do and when they are going to do it. That is not to say there is no improvisation, Bruce Springsteen comes to mind. But normally there is something programed for those improvisations. Sometimes there isn't, and you just run on the fly. With rigs as big as that, people really aren't going to notice if something is off and likewise the designer/op probably knows the band well enough it is.
Track acts it is simple to sync things to. They have to do exactly like the track and keep on beat with the track. This is one of the reasons I love doing dance shows because it can be sync very easily since the dances don't have a choice but to do what the track is telling them to do. I am notorious for syncing shows to tracks via timing. Once I did a number called "Stomp to My Beat" (can find the track on YouTube) and sync a light change to each beat. The track also stopped at 2:09 fortunately. It was done with nothing but conventional lighting and some strobes. After the number, my one friend said to me, "Thanks for the seizure." So it can be synced without midi or time code, but you need to be touring with the band or on tracks. Otherwise, you are really just busking.