Should be just as easy. You'll notice when you take the stock midpipes off they have brackets in the same place (extra support because the cats are pretty heavy). Bypass pipes are pretty light so those plates become kind of superfluous. I guess circuit werks included them anyways. Use them if they line up nicely and it makes you feel better. If they're making aligning the rest of the pipe a pain, I don't see any harm in chopping them off.
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