Bottom of the BB, ie: underneath so the water can fall out*, 4-5mm should do it, and yes it will probably technically void your warranty.
*Not 100% clear from your OP if you mean water is settling in the BB area, or in the bottom of the downtube. have a look in there, if water in the downtube can freely flow to the bottom of the BB then you’re OK with the above, but if there are any steps/lips etc that would prevent the water getting to the bottom of the BB shell then you may have to get creative.
If it was my frame I’d do it, but I’m not going to recommend someone to void their warranty and drill holes in a frame if you’re not comforatble doing it. Silicone sealant, rubber gaskets and regular inspection and maintenance are your other option.