I got a new pb in Random seed solo any% structureless obtain cake speedrunning. However, I end up finding a ruined portal at spawn. I never actually use it in the run, only putting chickens in a hole next to it to keep them from despawning. Is my run automatically invalidated because of that?

If you didn't use any block from the ruined portal or loot the chest there, then the run would be count as structureless. If you use, for example, netherrack or magma block from the ruined portal for something in the run, it would be count as structure run.