MetalJer: You apparently have the same press I do--the 'standard' in a 4-die configuration.
1. Yes, it is normal for the indexing rod to float. In floating, the inertia / momentum (take your pick of analysis) issues the forces involved in rotation introduce twisting--and since the base of the rod is free floating, it moves off the dimple. It's completely normal, and it really has no significant impact on your cartridge-building. Likewise, there will probably be a 'twisting' in the base--i.e., where the ratchet is. It would be nice, I guess, if it didn't twist--but it will, and tightening the clamp some more won't solve it in the long run. Again, it's not an issue.
2. Yes, the primer insertion lever is offset to the left about ten degrees. When / if you install the safety prime, you will see that the offset helps keep the lever accessible.
As for tweaking and adjusting the indexing. As RustyFN tactfully pointed out, you can't identify any final tweaking needs until you start working with cases.
As you go about trying the different steps in reloading, you will find that you are both consciously and unconsciously learning how to stroke the press lever. As you learn this, you will adapt to the different pressures needed to successfully perform an operation. IOW, the feel of a stroke for the sizing-decapping is different from the feel of seating a bullet. Eventually, you will even be subconsciously speeding up and slowing down at different parts of a given operation. This is simply part of the learning curve as you learn to operate the press 'smoothly.' In fact, I suspect one may have problems if they even try to think too much about these stroke differences--it's a gestalt, I think.
As you acclimate to these different 'feel' characteristics, you will probably make a conscious decision to start speeding up. And, that is when your final tweaking can be done. At some point you will find that, given the rhythm you use (I tend to run about 180-200 rph in production mode), one stroke will consistently cause the turret to over-or-under index slightly. Unless you have very real problems with indexing early on, don't worry about tweaking. Get the indexing set so that the turret "falls in" just as you are near or at the end of the stroke.
It's time to try using the press--but not loading finished cartridges yet. Try removing the indexing rod and simply try a given operation--e.g., sizing. After seeing the die is adjusted properly for full desizing, then size at least 10 or 20 cases to get a feel for it.
Don't worry about priming at this point, or about the Safety Prime if you have it installed.
Take those same cases and try PTED operation and adjustment. (this would be the 'startup' workflow for handgun and the smaller rifle calibers; you didn't say what cartridge you are working with. RustyFN will fill in on rifles--I'm a novice rifle reloader except for a small amount of .223).
And so on. Check back in with questions as needed.
editingfx: I consider about 3% spillage (with #5) to be about normal, I think. If you keep a clean bench, you can even sweep it up for reuse....
Jim H.