Air Carrier Captain reported they were on the runway in position and holding when an arriving aircraft on short final executed a go around and overflew them.

Narrative

We were cleared to line up and wait on Rwy 3R for departure after the traffic on final". There was Aircraft Z on approximately 3 mile final we saw visually and on TCAS. Person A though this clearance seemed very nonstandard we accepted and lined up after the traffic landed. We cleared visually and on TCAS and didn't see any other aircraft for 3R.While we were waiting to get takeoff clearance; I noticed another aircraft behind and above us on TCAS while we were on the runway awaiting takeoff clearance. The tower controller was speaking Spanish so I couldn't understand what was said but the TCAS traffic was Aircraft Y that executed a go around at approximately 700 feet and overflew us in the takeoff position. Nothing was said to us and after the go around Aircraft Y was clear we were cleared for takeoff without any comment or incident. I am confident we complied with the Towers instructions and were not at fault at all; but it is unsafe to issue clearances onto runways with any aircraft on final that you need to sequence behind. It's especially unsafe if there are more than 1 aircraft on final that you are not made aware of."