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For full context: http://www3.nhk.or.jp/news/easy/k10011273631000/k10011273631000.html

The sentence in question: 水族館の人は、「ペンギンはくちばしを空に向けて大きな声で鳴いたあと、頭を下げます。それが神社でお参りしているように見えます」と話していました。

My attempt at translation: "An employee of the aquarium said 'After the penguins had sung with a strong voice with their muzzle pointed towards the sky, they lowered their heads. This seems like they are worshipping at the shrine.'"

I couldn't come up with an interpretation making more sense than this one. However, especially since が instead of は is used in それが神社でお参りしているように見えます, I'm not sure if my translation is legit. I'm not very good in distinguishing where は instead of が should be used or vice versa, but since が is oftentimes used when something is newly introduced into the universe of discourse, I was surprised to see it in use here because what this それが points back to isn't new in this conversation.

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As for translating ように見える, it's better to use "looks like" because the speaker is not wondering if it's a fact or not.

As for the rest, from a different angle, what if the sentence was ペンギンは、…鳴いたあと頭を下げるのが 神社でお参りしているように見える?

It's a bit too long, isn't it? Why don't you split it? I mean, ペンギンは…鳴いたあと頭を下げる。それが…お参りしてるように見える. See? That's the example sentence as it is.

As you see, what それ indicates is a new information, hence doesn't really need to be further topicalized under the primary topic ペンギン.

(If you nevertheless do it, that's in general considered a bad composition because it could sound as if the topic is shifted from ペンギン to something else, which feels loose or distracted. That's why we are taught to avoid it for good composition. In other words, it's so natural for native speakers that you need education to stop it. p.s In this regard, a sentence that has two primary topics can't avoid it.)

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