Mainly with EMIs.
When the bank asks for registered address, provide the address in Estonia.
When they ask about place of operations, answer truthfully. If you're operating from home in Spain, that's the address you'd provide.
Yes, but that's not really specific to EMIs nor to Estonian companies.
If company and UBO︁ are in the same country, it's better than when they aren't. But it's not a︂ firm requirement. Banks look at the application as a whole.