AnotherGame is a mod for ToE 3.1.

The idea arose of alternative buildings in the city. For example, either a warehouse or a capitol.

So, first we create a problem (free warehouses, which open access to free mine development), and then we will solve it by imposing various restrictions on the capitol, etc.? Interesting approach.

And what prevents another player from doing the same?

I repeat, the concept of "balance" is broader than you think. For example, you can lower some alt-upgrades to an unacceptably low level, and no one will choose them, but the "balance" in your sense will not suffer, because the faction as a whole will maintain its overall statistics due to other upgrades. Balance is also about equal choice, which you will not have (converting dwellings will happen almost automatically, just like in Heroes 6).

In addition, the upgrade can be completely prohibited without building a warehouse (hereinafter "workshop" - well, you can rename it that way).

This is already a more mature idea than discounts.