What is your source that they are almost equal of Custodes?
I am genuinely curious because I would say even a Space Marine would easily win against a regular Sister of Silence.
They are of course really effective against Pyskers though.
They are always deployed either against Psykers (Burning of Prospero) or Deamons.
As far as I know they are not augmented and are only stronger because of their power armour which increases the wielders strength considerably.
Their training is really intense and they are probably the top of baseline human female physique. Adding to the fact that they are all nulls which unsettles even normal humans and is extremely torturing for a Psyker to be around, I would wager that also makes them slightly more effective than usual even against non Psykers.
There are a couple highly skilled individuals within the Sisters of Silence though, but that goes for all Imperial organisations and should not be taken as the baseline for comparison. (A Lucifer Black was skilled enough to wound Alpharius in solo combat, Lucifer Black's are normal humans without modification).
Primarch > Custodes > Asartes > Sisters > rest of the Imperial military.