fixes some stuff, note that the infinite loop is still present but only mitigated

code/modules/maps/map_template.dm

@@ -103,13 +103,15 @@
 			machines += A
 		if(istype(A,/obj/effect/landmark/map_load_mark))
 			LAZYADD(subtemplates_to_spawn, A)
+		if(A.initialized)
+			atoms -= A
 
 	var/notsuspended
 	if(!SSmachinery.suspended)
 		SSmachinery.suspend()
 		notsuspended = TRUE
 
-	SSatoms.InitializeAtoms() // The atoms should have been getting queued there. This flushes the queue.
+	SSatoms.InitializeAtoms(atoms) // The atoms should have been getting queued there. This flushes the queue.
 
 	SSmachinery.setup_template_powernets(cables)
 	SSmachinery.setup_atmos_machinery(atmos_machines)

code/modules/maps/reader.dm

@@ -377,8 +377,8 @@ var/global/dmm_suite/preloader/_preloader = new
 		SSatoms.map_loader_begin()
 
 /dmm_suite/proc/create_atom(path, crds)
-	set waitfor = FALSE
-	. = new path (crds)
+	// Doing this async is impossible, as we must return the ref.
+	return new path (crds)
 
 //text trimming (both directions) helper proc
 //optionally removes quotes before and after the text (for variable name)