I tried to use the Resource Removal mod today, but it's unclear how to use it. Furthermore, it seems like it might be outdated and busted.
Instead, I used this mod - Generic Object Remover
https://www.nexusmods.com/valheim/mods/1274

It immediately let me clear out an indestructible tree in the Swamp that was blocking a Muddy Scrap Pile from being fully harvested.
Simple to use with the in-game console (and great instructions on the Mod page).
Hope this helps anyone else in the future!