When using the right-click-to-harvest functionality from TinyTweaks, Tomatoes only break/replant half of the block, leaving half floating, and can also "replant" in the air. I don't know if this is an issue with how TinyTweaks implements its harvest functionality, or an issue with how CE:F implements the two-high crop.

Made an issue there too. Will try to keep up-to-date on both, and will close if it's solved on either side.
Haven-King/TinyTweaks#69

Tell me if it still occurs in v1.1.4 (when it will be up).

Unfortunately it's only partially fixed. When the top half is harvested, the entire crop does break as intended now (though doesn't get replanted- this part would need to be implemented on TinyTweaks end I imagine) but the issue still occurs when the bottom half is harvested instead.