I am rather surprised to read that the bottles have been confiscated and I presume that this was related to the limited knowledge of the customs agent.
I cannot speak for the Netherlands, but in Switzerland the limit is also 1 L free of VAT and duty. You can take more than 1 L of spirit with you, but then you have to pay the VAT and the duty for all the extra. In case of a fine, the fine will be calculated on the same basis.
For Sweden, for bottles sent by post, I have heard such stories about confiscation. Anyone has more info?