1. He graduated from it in 2009. He graduated in it in 2009, would specify a major you might've graduated in, so it might be conflating in its passing impression, burdening readability. 2. So your contention being that a university isn't just a place but an institution imparting education and by that merit an entity, I get that. You've got yourself a legit concern and query, so here goes. 3. For entities we also use ' there '. (4) He worked at Microsoft ( not, he worked at it! ), he worked there, he was fired from there. So now we're clear with that : )

Well, I think you can put the word 'it' between 'from' and 'in.' But 'there' is more natural than 'it' because 'there' means 'the place' or 'existence' only, however 'it' has other meanings so that it may lead some listeners have a mind that 'Did you say 'it?' Hmm.. okay, though there's the better word 'there,' that is right, too.' So, you should write 'there' instead of 'it' in that sentence.

Tricky one. It’s to do with usage more than a rule. I graduated from University of X. I graduated from there in 2017. ( a place as well as a school )

Thank you very much for your kind help. It helped me very well.

We use "it" if we refer to a thing while "there" if we refer to a place. So using "there" is more appropriate. Let's have this example. I live in Russia. You say, I live there, too. You can't say I live it, too. Right? Second, you can also omit/remove "from" in the sentence. He graduated there in 2014. Hope it would help you.