You are seriously overthinking this. The only part you have to handle with care is the primer. If you hope to practice priming with spent primers prepare for frustration. They will be deformed and will not easily go back into the primer pocket. Just use a live one and take care to have it square in the seating tool and the case properly centered in the case holder. If you feel excessive resistance back off and check the alignment again.
Primers are set off by being struck. A slow push is not going to ignite them.
Smokeless powder is not the same as black powder. BP is an explosive, modern smokeless powder just burns really quickly. It will not ignite unless you introduce a source of ignition. Don't smoke while you're making ammo and don't do it by candlelight. You'll be fine.
To check your charge, throw a charge and weigh it. Then put the powder back in your hopper. Repeat at least 5 times before you even think of seating a bullet. The charges should all weigh the same. If they don't you need to fix your powder thrower before moving on.
As you work through a batch, re-check the weight of the thrown charge every 10-20 rounds to make sure it is still correct. Toss the weighed powder back in the hopper - do not try to get it back in the case.