Bridge Edge Loops creates unnecessary tunnel hole

I am trying to cut 2 holes through this hollow-like object and after using the Mesh Knive Project on my object along with the circle, I’m now using Bridge Edge Loops and noticed a “tunnel” being made from one end to the other. While I could re-enable Cube.001 and use the boolean modifier to cut through the tunnel as I initially did to get this object, I would like to know if there is an easy way to only cut the holes through the object walls and not create the tunnel in the first place.

I just realized that I do not need to use Bridge Edge Loops as I can delete the faces I get from the Mesh Knive Project tool.

I still wonder how can I go back to a flat surface after I cut the holes with the Mesh Knive Project, other than going back with Ctrl + Z.