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

Yes, in 1.38.3 the library slot does not get rebuilt.
I.e., it needs to be rebuilt, right?

Naturally. No one has revoked the HeroesWorld rules. By default, the library must be rebuilt. This is not just a feature; it is a long-established game balance, and changing it is absolutely not allowed (at least without massive, multi-day discussions and votes).
Tower is already one of the weakest factions, even on the 6lm10a template, where the Mage Guild is extremely important, very few people trade for Tower even with a rebuildable library.

Bans on library rebuilding are rare, and only in specific tournaments; whether to introduce a checkbox or not is a completely different matter.

Added after 8 minutes

For example, does anyone play without the chess timer now?
And does anyone disable the "start timer after turn confirmation" checkbox?
Or the "retryable quick combat" checkbox?

I can decide on those myself, but what about the HeroesWorld rules checkboxes?

So which checkboxes should not be in view?

Only noobs from the lobby who are unfamiliar with HeroesWorld (and love the 2-4 min timer) play without the chess timer, but I think that's their right (there are quite a lot of them).
I think "start timer after turn confirmation" and "retryable quick combat" can be made default and the checkboxes removed.

The HeroesWorld rules checkbox should remain; it is unchecked when playing without rules (not necessarily the Anarchy template).

I think the checkboxes for cartographers, hill forts, and keymasters can be removed (when HeroesWorld rules are enabled, they simply should not appear on the map); when the rules are disabled, they should appear.