The Mortarchs come on a large base and are a much larger model, so whether you measure base-to-base or model-to-model, you're at a slight disadvantage by using a Mortarch. When that's the case, I would have no problem with someone using that model as a "counts-as" replacement. I even use Nagash as my C'tan Shard of the Nightbringer in 40k, and I've yet to have a tournament refuse to allow it. You can usually scale up, but not down.
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