The ones I have worked on in the past I ran through the curb. Problem is how these sit conduit needed to be run while they sat the units on the curb. We didn’t know what day they were setting them. Anyways. 6” away from unit should be clear from any flashing that was installed from the curb
What you should be doing is finding out who the roofer is from the guys that are setting the units and curbs, tell them how many roof booties you need for your penetrations or if you need pitch (tar) boxes for asphalt built up roofs. Have the contractor setting the equipment get the required booties or boxes from their roofer to match the material that roof is made of.
Then you place the provided booties over your conduits when your installing them. Place the booties or pitch boxes over your conduits as your installing them. Make your penetration hole just big enough for your conduit, then it can be temporarily sealed with roofing caulk. Leave the boots raised up on the conduits for the roofer, then have the HVAC contractor call the roofer to come and provide the final seal up. This way you wont void any roof warranty or be responsible for any leaks now or in the future.
Going through the roof underneath the curb and equipment is the best way and avoids most penetrations that need to be sealed by the roofer. But to do that you will need long pilot bits to mark your penetration location, and some hole saw extensions to reach from the curb height to the roof surface.
The same type method can normally used on the exhaust fan curb, but most exhaust fans need a flex whip installed above the curb in order to hinge the fan open for cleaning. Locate your required disconnect on the side of the fan curb.
