Hi Jeff,
IMO you don't have to worry about the stand touching the neck and exerting pressure. The stress on the neck(joint) is way larger when you would hang the guitar by its headstock on a wall bracket. And that is no problem for a guitar either. So then the choice comes down to safety. Personally, I like the neck support because it is so much harder (not impossible) to tip over the guitar. But you hardly can go wrong with with either of the 3 options you describe.
A different thing is leaving your guitar permanently in a stand. Especially for nitro finished guitars there are stories of discoloration due to interactions between the finish and the (neoprene) rubber sleeves and even deformation due to the finish flowing around the pressure point (see e.g. this
post in a different forum. I believe this is less of a concern with polyurethane finishes.
Hope this helps,
- Jos