Hi @kenny.dgolmos01,
Welcome to our community forum!
Yep, in the Base settings the height should be ellipsoidal. But as Javier showed, when you collect the points in Emlid Flow in a project with a specified projection and geoid, you get both local and global coordinates with ellipsoid and orthometric heights.
By the way, we have a couple of posts that can help you set the base in Emlid Flow: