HoMM3 HD is a mod (add-on) for the game Heroes of Might and Magic 3.

Honestly, I don't understand what you're talking about.
1. Why would I cut all of this out?

No one is saying that it was cut out. The problems and reasons are being clarified. This means that some kind of add-on was inserted, which also eliminates the necessary properties.
When moving the cursor over visited magic shrines, witch huts (and possibly other objects) during the opponent's turn, the "visited/not visited" label and the name of the magic or skill are now missing.

2. I have never observed this during testing (including after reading this report).

I'm just curious, do you play baratorch online? Maybe that's why you don't see the problematic moments. Such nuances are added in online mode.
Previously, when visiting a gem garden or a mine, a window with the corresponding message would pop up. Now the window does not appear (as in WOT). I don't think this is how it was intended.

I can easily revert to the old functions, and attach the new one to Alt, but I don't really want to, I don't see anything terribly critical in their absence.

In this case, it is important to separate the units immediately from a large stack of low-level units from one hero to another before taking the lair, for example. Just restore the old Ctrl function when transferring troops, and it doesn't matter how it is attached. Manipulations during transfers really take a lot of time. This is not noticeable at all in offline mode.

All the other features of version 3 already more than compensate for this, if you can call it a drawback. Is it really necessary to use them so often? Does their absence make the game impossible? We should bury the original Heroes altogether, there are not only these functions missing there.

After all, it is clear that when you get used to something more convenient, you don't want to go back to the old. But errors are inevitable. And you need to stop in order to fix them. And refine what already exists. For example, make it possible to quickly transfer troops from a hero to a city, garrison, or mine.