Haven't tested this one yet but Object Deleter mod appears to be a thing. https://www.nexusmods.com/valheim/mods/1273

But yeah, build everything on raised foundations, with corner pilings driven solidly down into the terrain it's the best way to get symmetrical stability all the way around. Easy upgrade to stone later too.

Oh, also you can just dig a hole under the dandelion, its spawn point will sink with the ground level. Or raise it and build a little planter. :D

TBF Dandelions are about this annoying and persistent IRL.