If you mean something like this ... Cube with Empty as Instance ...

To Apply modifier failed for me so I exported as Alembic (.abc) and Imported back with realised Empties as expected or even better all Empties are parented to the Cube object that is now just an container without any vertex.

If you mean something like this ... Cube with Empties - enable As Instance under Object Info node ...

To realise instances ...

You can Ctrl+A > Make Instances Real, which will create individual Empty objects at those points (the GN object will still be there, modifier still on it, it won't be applied).
(Credit goes to Kuboå :) I just wanted to highlighted his comment here.)

I exported object with GN modifier as Alembic (.abc) and Imported back. Realised Empties come as parented to the Cube object that is now just an container without any vertex.

If you mean something like this ... Cube with Empty as Instance ...

To Apply modifier failed for me so I exported as Alembic (.abc) and Imported back with realised Empties as expected.

If you mean something like this ... Cube with Empty as Instance ...

To Apply modifier failed for me so I exported as Alembic (.abc) and Imported back with realised Empties as expected or even better all Empties are parented to the Cube object that is now just an container without any vertex.