Transfer punch sets are great in their place.I think they have limited use for gunsmithing.One issue would be they are typically fractional.Tap drill sizes for sights would typically be of a number drill size.
I would use a trasfer punch to make a very light layout mark.I do not use them as a center punch.
I realize old school machinists and gunsmiths did use layouts,center punch marks,and drill presses.They created a lot of problems that way,too.
The web,or chisel center point of a twist drill has,for practical purposes,no cutter speed and little cutting edge.It is a problem that causes a drill to wander.Add to that a twist drill is flexible.
I recomend against using a center punch mark.
Get a good,small center drill,a number 1 or 2.Look for a 3/16 body dia.
Now,if your chuck wobbles,dont use a center drill,you will break it.Go with a spotter drill.To see/buy these,go to MSC or Enco.Browse around.
These stubby drills will make a real nice start for your tap drill.The web of the tap drill touches nothing till the body of the drill is guided by the hole.Use a center drill and drill right,and your hole will not wander .001.A center punch mark will not be perfectly under the center of the spindle.It will deflect the drill,and the hole will be out of square.
You do need a vise,and the vise need to be clamped down.It will take patience to get the hole lined up and clamp down the vise.Use a little dead blow hammer to slap it around a bit.
Actually,if you use a pin or dowel a bit smaller than your base holes,your eye can center pretty close.Look from different angles.I use a Browne and Sharpe .0005 test indicator to spin in the hole till the needle does not move.Then I know I am centered.I do not do trailer hitch grade gunwork.
At this point,I'd do one end screw with your base clamped in place some how.I have even used superglue.That is not a recomendation,just gitterdun.
Center up on the hole however you will.Now,without moving anything,center drill,tap drill,lightly chamfer,then tap your hole,all on one location.
Then clean up and deburr.Now,use that one screw hole to attach your base.Your screw should center on the hole.Now,you know that one lines up.
Carefully position and clamp the other end,and drill and tap the other end hole
Then put another screw in,and finish.
Or,you could take a piece of steel stock,practice transfering the holes to that steel stock and tap drillng your practice piece.Do it till you get 4 precise holes that line up.Clamp that to your reciever and use it for a drill fixture.It will guide your drill just fine.