This seems to have to do with Multiblock: Frames wire can be placed in the same block as a gate (see below). Depending on the gate, some have bad visual collisions.

Also, see my super-slate-cell :)

There isn't anything that can be done about this.

The size of the gate could be extended as high as the tallest torch, but I don't think that is a good solution either.

There is absolutely no way we can take into account every single permutation of gates, their rotations, and their states. Like is said, NOTHING can be done about this, unfortunately.

To clarify, something could be done but it would reduce the building
possibilities.