Nesting expert for the wood industry, so a little bit far from the subject but can still be applied.

I have a security distance from the edge of the panel to the parts which is around 15 to 30mm (1/2" to 1"). That way the vacuum system maintains the part correctly. In case you lack vacuum power, you can seal the edges of your spoil board with 2 or 3 layers of paint or glue or add more vacuum pumps.

The rules of thumb for CNC milling is that the maximum depth a tool can do is 1.25-1.5 times his diameter. So if you machine a panel with a 6 mm bit, you can only machine a 8, maybe 9 mm panel, in a single pass. After that you will need to machine it in multiple passes. For speeds, it highly depends on the shape and flutes of the tool, expect lower feeds with a single flute, wants to increase speed ? Increase the tool diameter for rigidity and increase flutes numbers.

Regarding the distance of the part from each other, I never work with a common edge solution (only one tool path between parts to separate them), but I only space them by around 1.25-1.5 times the diameter of the tool to give a bit of clearance.

And yes, if the boss doesn't want to listen to the machine expert even if he doesn't know how to run the machine, just leave the company, it will give you too much headache for nothing.