Thanks for looking into this @johnsonshiue .
For Problem #1, the designer was inattentive and did not correct the tap that INVENTOR chose by default (he did not choose the tap, Inventor did, and he did not CORRECT the tap that was presented ... result: we received an incorrect part that was our fault - both the designer and checker missed the inconsistency).
My reason for posting is that, when applying a thread feature to an existing hole, Inventor should choose, by default, the tap where the MINOR thread diameter is the hole diameter. If you choose a tap for the hole which matches the MAJOR thread diameter, there is no material available to thread (Inventor shows the graphical thread feature but, in reality, an actual tap of the selected size would tap only air).
As I said earlier, the converse is true for external threads (the MAJOR thread diameter should match the existing outer diameter and yield the default thread size presented by Inventor).
For Problem #2, @johnsonshiue implies that the designer is not following the proper workflow. Personally, I would have created a double tapped hole this same way. I would NOT have used two hole features (one from each side). Is the latter what is envisioned as the proper Inventor workflow (using two hole features)?
To make this feature in a shop, they would drill THRU (once) with the tapping hole size THEN tap each end. This matches the hole and thread feature sequence that was applied by the designer (and what I would have done also). Using two hole features is like drilling twice and tapping (obviously a shop would not do this). To me it seems most logical that the hole note attached to a hole feature should have the drill thru information while the hole note attached to a thread feature should have only the tap and the depth of the tap.
Separate issue (FYI): When I download purchased part models which have tapers for NPT (male or female) or worse, with cut threads, I like to (delete the cut threads and) add the Inventor tap feature before checking the part in. I have noted that Inventor never picks the appropriate NPT tap size, even when the tapers are correct. This may be related to the above.
Now I throw down the gauntlet ... I understand that Solidworks has a very robust hole feature where you can combine multiple hole-type features into one. I wish for this every time I have to use multiple, separate hole features to achieve what I require. For example, a spotface with a counterbore and a thread (e.g., bolting something to the spotface with a shoulder bolt where the shoulder is embeded into the counterbore). While this is just an extra step in the solid model, detailing this in a drawing is a little more difficult. I think this is a worthy challenge for the developers. Note: The double tapped hole discussed above is different because it is not all happening from the same side.
Inventor Pro / Vault Basic