Firstly, unless your guitar is locking bridge type (floyd rose), you must be nuts to put the ball end on the tuner end.
Secondly, I don't see the problem with the ball end at the tuner, provided you cutoff the ball itself. You must also trim off before those wire wound start (the bare part of the low fatter strings, E A D).
Thirdly, if you use the ball as a stop (start exact where the ball is, and leave it there). Its quite dumb too as the string can wrap around the ball itself and you get inconsistent tension as you tune.
Forthly, it's up to your guitar string change skill, if you are good, I don't think it matters. If not, learn from someone who is good. Remember, the ideal when in tune is for the tuner to have 2-4turns on it.
Neck warp is subjective, if the neck is constructed well, should be no problem. More likely you will encounter your hardware (metal) & electronics parts will suffer if you leave the guitar open on a stand for prolong periods like 6 months without touching it.
If it's poorly built and suppose to warp after a while (some really do), you can have 0 gravity suspension and it will still warp.