For the deconstruction planner, even vanilla ores (e.g., iron-ore, coal) cannot be set as whitelist/blacklist filters. The game mainly deals with entities, but not to distinguish items on ground. So it is vanilla GUI design problem, not my fault. You should report to Factorio official forum, if you think it is an issue.
"Upper part of tower" remained after removal definitely means some mod(s) have overridden my removal script.
This mod list is too long for me, I would not have such plenty of time to test them. So you have to try to isolate out which mod(s) maybe causing the conflict. Please do the following steps:
1/ Start with your mod set, with this mod (Schall Pickup Tower) enabled.
2/ Pick a mod to disable, starting with the most susceptible mod that you think could be the culprit. (Calling it "mod A" in the following .)
3/ Enter the game. Check if having any problems you mentioned (like blueprint problem, remnant problem, etc.).
4/ If still yes, then select the next mod to disable. (Calling this as "mod B", "mod C", ..., vice versa. So now from "mod A" to last chosen mod are disabled.)
5/ Repeat from 3, until the problems are gone.
6/ Now the conflicting mod(s) must be within those you have disabled. Mark this list down.
7/ Reenable all mods again. Repeat from 2, but this time only pick mods from this conflicting mods list to get disabled.
8/ Try to narrow down the conflicting mods list as much as possible. (I guess only 1 or 2 mods are truly responsible.)
9/ Send me the final conflicting mods list here. It would be reduce a lot of my workload, if I only have to check the code of 1 or 2 conflicting mods.