[masaegu]

Yes, that is correct.

In your first sentence, the most important part is the 'koko' and not the 'isu' because the person asking the question 'Where is the chair' is asking for the chair's location. The person answering could have just replied, "Koko ni arimasu" (= It's here.)

But in the sentence "Isu ga koko ni arimasu", the subjet 'isu' is the most important element of the sentence as the question is "What is there?" It's not a desk or pc or fridge. It's a chair that is there. That is the hidden meaning of 'ga'.