Sorry it took me so long to hunt down the answers to these questions, but it takes a while to remember some 10+ years of knowledge and make sure its accurate:

1.   SR generally does not include time spent in menus, cutscenes or loading. This will largely account for the couple of minutes per hour the community is seeing.
   

2.   Because we do not count time in cutscenes most should start after the opening cutscene. The time will generally start when the player is given control. This was never tested but holds to the logic.
   

3.  The Australian release of Saints Row IV is censored with Shaundi’s loyalty mission disabled, so that would be a time advantage . The Saints Row 2 German release had some minor gameplay changes with not being able to execute the prison doctor at the start of the first mission, and higher notoriety gained for killing police. All other SKUs have only had art and dialogue changed to fit into country guidelines. 
   

4.   There is no appreciable difference in framerate between regions. Most different regions are straight text changes.
   

From SR1

1.   Pushbacks have a cooldown and occur against a Saints area bordered by a rival gang. Based on what is owned and the position of the player these can be softly manipulated. This is why routing the game would give fairly consistent results. Generally they cannot be avoided.
   

From SR2

1.   We discuss some of the vehicle spawn system in the email.
   

2.   Missions will have spawn rates for vehicles that are pertinent to the mission. They will however reset the NPC vehicles that may have blocked the Tornado from spawning the first time.
   

3.   The wiretaps are inside an interior which causes some outside areas to unload. This in turn would cause some NPC controlled vehicles to despawn. This leads us back to the same principles that the vehicle may now spawn in a spot that was freed.
   

4.   This is likely due to flying. The Tornado was not a widely used vehicle during testing. The cargo boat is a special mission. 
   

5.  This is not by design
   

6. Also, not by design. Sounds like a glitch.

From SR3

1.   There was no patch to address this. This is likely due to the amount of memory a PC has. 
   

2.   Can’t find a quick video of this. Not entirely sure what is happening when it occurs. With a video of the entire fight before the problem we may be able to give more info.
   

3.   Sounds like a flag is not cleared when saving/loading. As you have already said it’s not particularly useful in a full run.
   

From SR4 4. During testing 100% was defined as all missions, collectibles and challenges being completed. This takes quite a bit of time to complete. 5. As I recall SR4 always warps the player back to the same spot in the city. Each area outside the world should also be encased entirely in collision making it nearly worthless to know where they are as crossing through those would not be possible. The ship should also be down there but again it’s not possible to enter from the outside as far as I know.