When sitting, the waist of a guitar needs to be either on the left thigh (classical style) or right thigh (most people's preferred). Ironically, when standing it rest in neither of these places when strapped on - it's between the two. People who do most of their practice sitting then have to adjust when strapped on. The other aspect is the height of the guitar when sitting, compared with standing. Often it's lower when standing - again changing angles of fretting arm in particular.
The neck waving about is not going to be a problem - find your own optimum position. I actually play with the neck at about 10 or 11 o'clock, if I face 12 o'clock, particularly seated.
If you wanted, you could of course have the strap on while you are sitting down - quite a few players prefer this.It's not like a bank of violinists who all have to be the same. With guitar, right and wrong are not as important as comfort.