AnotherGame is a mod for ToE 3.1.

You don't understand.
I gave you specific examples from in-game situations. The choice is between a town hall or developing a gold mine. Naturally, the town hall, because it's cheaper. The choice is between a warehouse or developing a resource mine for the same resource. Naturally, the warehouse, because it's cheaper. Do you understand what I'm getting at?

The Town Hall branch – the Capitol is unique in itself, just like the Capitol itself, because you can't build another branch like it, and you can't build another Capitol either ;)
And what you're saying is something else entirely.

After the first week, an Elf can perfectly well manage with regular wood production, so there's no need to overpay for it.

Added 6 minutes later
I calculated that an Elf needs only 12 more wood to fully build everything compared to, for example, a Human castle. And wood isn't exactly in short supply there. So, is it worth paying 7500 for those 12 wood?

Are you resorting to relativity? Instead, calculate how much will be lacking during normal castle construction, without comparing it to any race. That will be more accurate. Humans sometimes lack stone, and less often, wood.
I'll repeat myself, but try to put it in other words:
Upgrading mines shouldn't become the norm. Have you even played on maps from IRMG? What's the point of uniqueness then?
Everyone builds a Capitol. In this regard, it's not unique, even though it's unique for the player as the only building.
For small maps, 5000 will be optimal; for large maps, even 10,000 will be too little. Don't forget about the conversion, which gives you a chance to build a second castle ;). The average will definitely not be around 5000, and this is also a plus to what I said.