I can't speak to the Indian rules specifically, but most countries would require you to at least disclose to the tax office that you are the UBO of the Estonian company.
And yes, if it's just you, then it will usually be seen as a local company from a tax perspective.
If you're only a passive owner (you have hired a CEO outside India to manage the business), then they may accept it - but they may ask for more documentation, and if the CEO is paid a $100 salary generating $1M in profit per year for the company, they will soon conclude that he's just a nominee and that it's really you who is running the company from India.
And even if they do accept everything, the company might still be a CFC - but I don't know the Indian CFC rules. If it's actually an operative business, it probably wouldn't be a CFC.
Anyway, long story short: You can't be involved in the business from India. You can only be a passive owner, and you have to be able to prove that.
I also wouldn't necessarily recommend
Estonia, but that's a different story.