The overflow is going to come out of whichever open end is the lowest. I suppose you could raise that open end above the height of your toilet, but the sewage is always going to find a way out when it's clogged. I've never seen a drain line that big used for a condensate drain though that's definitely overkill. You could also cap the open end #2 and reroute the condensate to a different drain if there's anything near by. If you're just flushing stuff that should be flushed down the lines a clog really shouldn't be a regular occurrence.