I downloaded Stake and I see what you're saying, but your own post alone should have tipped you off that something was wrong. The reason Stake is set up in a 32x32 fashion is because CV1 stages were comprised of copy-and-paste 32x32 sections. By all means, go ahead and do that yourself, but the block tiles must always be aligned properly or else the game, not just my engine, will glitch. The fact of the matter remains you're still designing the room wrong if a block isn't placed at (0,0) or (16,16) in the TSA. A graphical glitch while running the game means your room is bugged, plain and simple.
I get what you're saying about making it more flexible and one of these days I might do that, but it doesn't change the fact:
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This arrangement is a valid NES block arrangement in all CV games
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This is not a valid arrangement. Period.
Even Rondo Of Blood holds to this rule of level design.