I would agree the second is more grammatically rigorous, and it's probably what you want to use if you're writing a paper or something. However, the first one is perfectly comprehensible. In casual speech and on the internet, you might even sound (or look) more natural using the first expression, since it has almost become a set phrase at this point. Great question!

Both are correct but, the second one "If only I had known then what I know now" is more grammatically correct. It is perfect to use if you are writing an essay.

"If only I knew" - you regret that you don't know something and you wish you knew it now ("If only I knew how to play the guitar" - you would like to know how to play it) "If only I had known" you regret now that you didn't know something in the past and you wish you knew it back then ("If only Kevin had been able to come" - Kevin wasn’t able to come) According to what I wrote above, I think the second sentence is more correct. Hope that helped you!

Both are grammatically correct, but Past Perfect is used as a past action or feeling prior to another past action. So it's correct to use the past perfect "If only I had known" but it would be useful to know what is the action related to the "if" sentence.