I use my vacuum pump to bottle all the time. I use the same stopper I use in my carboy to vacuum rack. You dont have to seat the stopper in the bottle, just hold it on top. No need to hold your finger over anything, just rock the stopper a bit to controle the flow. I can hold it on the top fully sealed with almost no pressure for a full flow, then just gently rock the stopper to get just a trickel when almost full. Lift up when full and vacuum is broken and flow stops. Only thing to remember is to have the full carboy below the level where you are filling bottles or else it will siphon..ooops..I dont keep the racking tube deep in the bottle I am filling because you then have to fill to almost the top because the hose displaces the wine and you wind up sucking some into the collection canister. I just fill to the shoulder and lift. Easy! And FAST!
This is the position for full flow..
And this is how I stop or lower the flow..