Personnaly, I don't think there is a right or wrong way of using the bags.
If all you can grow is 3 or 4 plants and your total harvest is about 200-400 grams.
Well using the bags as the stirring medium is still not a bad thing.
Naturaly your result will only be as good as the amount of agitation you can apply to the harvest (which is limited without tearing the bags).
Still not a bad thing, just limited in output.
I realise some people can only grow a few plants and this is where the bags shine.
As Nottheperson said so well, the purpose is to get as much from the sugar leaves as possible so there is no waste.
I grow 70-75 plants with a license, so the washing maching is not an option for me.
Needless to say, the end result is a little more using the machine and bags.