A block channel is always in some state, which includes all its settings, including on/off. Scene ignore keeps it from following scene changes, but doesn't uncouple on/off from the rest of the block's settings.
I'm not super familiar with scene controllers, but you * might * be able to use them to enable and disable a block per scene while it was set to scene ignore. I'm not sure about that, don't use them myself so far, and it's also possible that scene controllers just can't override bypass state, it's inherently controlled by scenes.
If that's the case, you might be able to use scene controllers to have the same effect as bypass, by controlling the mix parameter, or a separate vol/pan or multiplexer block.