That is the intended behavior. No matter who kills the Serco operatives or pirates in CCE, the mission should still advance. Anything else is a bug.

In the hazardous sight tree on the errant transport mission what is the best way to kill the infiltrater bot I can't seem to ever get close enough to them to kill one or they Dodge all my missiles

I've found that shooting just in front of it will cause the bot to slow down, making it easier to hit.

That mission map looks super useful in organizing missions. Did you make it after/before/during the mission making in pcc

These particular renderings I drew in PowerPoint after the trees were produced. I most often use a notepad (pencil and paper) during the conceptual phase and when testing.