Hmmm... It seems to me that you don't trust Inventor 🤔
You wrote in one sentence that the holes will be drilled/cut. But these are two different technologies.
Why is it so important?
If we are talking about cutting technology (e.g. laser), we can take into account all allowances and corrections at the modeling level. And very precisely. For this purpose, for example, the intersection command (necessarily from the inside to the outside) is used, which corrects the geometry of the hole so that it is accurate for the screw and at the same time understandable for the cutter.
PS. You can still use radial letup here, which will act in all directions even after rolling.
As you can see, the lack of intersection creates unnecessary misunderstandings that can be easily corrected and a nominal shape is obtained.
Another method is cutting (available in the sheet metal environment), where you can select the perpendicular cutting setting so that the program corrects the side surface in the direction normal to the sheet metal surface at the stage of this operation.
But this is all about preparing the model for the cutting process.
However, if you plan to make holes by drilling, you should prepare it in a different way.
In this case, you need to route (as with physical routing) the location of the hole using simple descriptive geometry.
For this we will use the existing sketch that was used in the base file for positioning the holes.
Since the marking tool does not work in a multi-body model (sic!), you will need to output this sketch to individual part files (two plates) by editing the derived part definition.
In this way, we obtain a model with a hole drilled in a flat sheet.
As you can see, anything is possible. Inventor can prepare geometry for many types of technological processes. It only requires conscious definition of these processes and conditions.
Everything else is limited to defining the appropriate dimensions and parameters.