the first question is purely depends upon your system, but in general the cleaner the boot is the quicker the startup will be, my answer otherwise is are you ready to drill or mill a hole in under 20 seconds of you turning on the lights were the mill is kept. I know it takes me at leaast 3-4 minutes just to figure out how to mount it in alot of cases. Just watch your hardware as there are a few computers(dell seems to be on top of that short list) out there that don't power the paralallel port to 5V and on all there models. Modders(the computer gear heads) have contests on how quick they can get there computers to boot, most down into the 10-15 second range(some quicker). I would alot arround 1 minute, this gives you time to turn on the lights, stepper drives, the radio and mount your work, I think you will find your computer waiting for you not vice versa. If you are one that works for 20 minutes walks away for 15 minutes and then comes back, I think you will find it easier on you and the computer just to leave it on, I leave my main computer for the house on. Since I have done that my power billl has gone up around $10 for a 500W power supply.
2. I think you will find that trying to set the machine to 0,0 by hand will be counter productive, esp since you have a button that does it for you. But to answer your question, when steppers power up they almost always cog to the nearest step, typically under 1.0 degree, on ultra sensitive machines you will notice a movement, I think on a x2 it will be next to nothing with stock screws. You will in the end find it alot easier to just not have handles, and rely on Mach to do the work, thus freeing your hands for more important things like, coffee(or soda) and the home shop machinst or local newspaper.
To give you an idea, I have a machine I work with that is an x,y,z,a vinyl die line cutter. It upon powerup if not homed will always move one step, this machine has encoders so it knows that its moved but it often looses that very first step so it often leads to after several(maybe 20) on-off cycles being off by about .005-.010" which is nomial for this app. But if its homed by the operator for what ever reason it returns to its proper alignment. I say this becuase with a stepper controler it only knows were it was, so if has been disturbed since its last known you may have undesired results should it power up and try to home or start a program without first homing. It would be to your benefit to give home limits, and you could also look into an MPG for manual overide, you will find this much easier then using hand wheels which can get caught on things and snap off. You could also create a pulse generator with some simple electronics I suppose, when you don't have the computer on, but would require a means of switching between the computer/breakout board and it. Again alot of redundant work unless you plan on not having the computer dedicated or always present.
I timed my kids smaller p3.0 1gig ram xp pro machine and it took it a marginal 36 seconds to get to the desktop with a password. I cannot even get a drill bit out and in the chuck in that time frame.