If using a 3mm cutter the code would give you a 3.6mm hole if runout is 0.
3.7mm if runout is 0.05mm.
The only way to get a 3mm hole from a 3mm cutter is a direct plunge.
Surprised fusion didn't tell you it's too large.
Use a 2.5mm with helix 0.25mm.
Still the issue around the edges though.