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As my experience with Heroes 3 shows, a draft of 18 castles doesn't change the essence. In any case, you end up with a limited selection of options.
On regular templates, the number of possible pairs is also not large, but here the decision-making space is even smaller - red will always have to eliminate Necropolis and Dungeon, and blue - Rampart and Swamp. That is, all the variability will boil down to choosing the 3rd castle, which also cannot be done in any way.
But with a two-sided draft, the number of options increases - the specified castles only need to be eliminated by one player, so pairs like red Dungeon vs. blue Rampart or red Castle vs. blue Swamp are possible.
As an option, simply make the secondaries identical - weak castles, like Tower, Barbarian, and something else. This will balance the draft: there will be an option to play with a strong castle or a weak castle with a double.