Everything is really based on the shoulder to base measurement. This is dictated by the headspace in the rifle. You set your resize die based on that headspace. Trimming the neck is only to keep it from hitting the end of the chamber. A little shorter is not the end of the world, but, too long and it will jam the neck in the throat and 'crimp' the bullet. Extreme cases cause big pressure spikes.

Since the headspace is based on base to shoulder measurement, then the simplest case length measurement is base to end of neck. As long as your cases are prepared the same, measuring/trimming based on the shoulder will get the same results as measuring/trimming based on the case base.

Bottom line. Set your trimmer of choice so the neck does not enter the throat. Do it the same for every cartridge case. Doesn't really matter how you accomplish that.