If I want 1ml I'll use the first line (on a 3ml barrel) as the start point instead of the 'whole syringe'. I'll draw to 1 line past the 1ml mark. Not easy to explain. This allows me to know that I have exactly 1ml. Anything left over in the needle or a drop that comes out when swapping is a minute amount.
What you refer is to called the dead space. The typical 3ml syringe that most of us use is going to have approx. .13ml of dead space. However, that amount is not calculated into the amount of oil in the barrel of the syringe. So if you intended to put 1ml in just draw to the 1ml line and you'll plunge 1ml in. Just be aware that 1.13ml is actually coming out of your vial.
This is a classic reason why so many guys think their UGL stuff is underfilled because they only get 9 1ml shots out of a 10ml vial but if you factor in dead space 9 x 1.13 = 10ml.
Some guys I know intentionally try to leave an air bubble at the bottom of the syringe so that dead space can be forced threw. Its a mixed approach though as there are negatives too.
At the end of the day just factor in that you're probably going to lose than tenth of a ml every shot. This is of course worse if you're only drawing out day .5ml versus 2ml at least in terms of percentage.