Its been a long time since I helped a buddy with his 6 mm but you are asking a pretty basic question - I think.
I believe you are asking if there will be a problem if the base of the bullet projects down below where the shoulder of the case becomes the case neck. NO.
Many factory cartridges (300 sav, 300 win mag, some 308 win loads, 264 win, some new short mags, etc) are loaded such that the bullet bases project below the case neck with no problem - as long as a proper load of powder is used and normal weight ranges of bullets are used - and the 95- 100 gr are pretty normal for the 6 mm.
Some folks don't like this situation and feel case designs that don't require bullets to sit this deep perform better. I think minor projection would not be a problem at all and may be more of a hairsplitting type argument. Maybe someone with a machine rest bench gun could detect a difference but you won't with a standard rifle.
Now if the bullet projects REALLY deep into th case - deeper than normal - then the net cartridge voulme is reduced and you may see increased pressures. But if you are following a load manual using normal wt bullets and powder and seated close to normal overall cartridge length, you'll be fine.
More importantly, I think would be to watch how close a bullet is seated to the beginning of the rifling. If you load such that the bullets engage the rifling when the case is chambered, you need to expect higher pressures for a given powder charge as there will be a lot more initial resistance for the bullet to overcome before it moves. Most folks load such that the bullet doesn't quite touch the rifling.
HTH