I use a mix of 3mm HSS twist drill in a standard 3mm collet to pilot holes (no spot drill), and then finish on the drill press. Or interpolate holes using a 6mm end mill ideally with a spiral toolpath. Fusion is great for this.

These end up being very accurate although for bolt clearance holes I often go for bolt nominal diameter plus 0.5 mm to give some allowance in assembly.

See examples in my videos here:

4:40 and 10:40
https://www.youtube.com/watch?v=wqff3IZZWvw