Inserting the following lines into control.lua after line 118 will stop the filtered deconstruction planner settings from affecting the behaviour of blueprint placement, namely that rocks and trees don't get deconstructed when you hold <shift>.
<pre>local stack = player.cursor_stack
if stack.valid_for_read then
if stack.name ~= "deconstruction-planner" then
return
end
end
</pre>