Thanks hogscraper. I still want it to obstruct, but only if it’s actually obstructed. I figured it out after two 10 hour days of staring at snap numbers and blueprints comparison.
For anyone that may find this helpful:
If you put the flag number of the thing you want to not be obstructing your structure in the “Trace Ignore Structures with Type Flags” box, it will ignore items with those flags when placing. I only found this out when I tracked down how foundations ignore the check for pillars.