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Actually, that's not a problem – the re-modernization coefficient can be adjusted in DefaultStats to 100%. Then, when upgrading to a more expensive creature, you'll pay 100% of the difference, and there's no abuse. And for switching to a cheaper option, no one is obliged to return money, of course :)
Added 5 minutes later
Creatures traditionally require gold, and building requires resources + gold, and why erase the difference between these two aspects of the economy.