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I know only a little about ETCS, but I believe that the answer to your question is no. The basic reason is that even the models of set theory themselves can differ vastly. If $M$ is a model of ZFC, then the category $Set^M$, which is Set as interpreted in $M$, will be a model of ETCS. But if ZFC is consistent, then the models of set theory $M$ are diverse. For example, some have CH and others have $\neg CH$, and furthermore, by the incompleteness theorem, they can satisfy different arithmetic statements. Such statements show up in the category $Set^M$, since I believe that every arithmetic statement (first order statement about natural numbers) has a translation into the formal language of ETCS. So in general they are not elementary equivalent. In general, you can expect no nice functors between such models, as some can have uncountable natural numbers object, and others not, and all kinds of crazy things. In general, it will not be possible to map the natural number object from one to the other in any nice way.