This arrangement of glass panes:

looks like this with CTM enabled:

There's a nice continuous border around the edges of the glass for the most part, but it terminates at two points.

The blue border is probably very easy to fix with model files alone and specific CTM for this texture (I myself have fixed this in a non-CTM context by redoing the models), but the red line would require that the pane should not only detect the presence of a glass pane above or below it, but also its connection type. To my knowledge, the mod does not currently allow for this.

Even OptiFine, with its #74 fix, is not immune to this problem, with textures connecting in sub-block places where they really should not:

I don't really know how complicated a fix for this would be, but it's something I'd like to see quite a lot since a fix for it and #74 would allow for absolutely perfect glass pane connections.

I believe this is the issue that sp614x/optifine#193 describes.

I've managed to seamlessly fix the blue border (#301), so red is the remaining one. We'd need panes to be able to accept separate "up_left", "up_right", "down_left" and "down_right" connections, rather than just "up" and "down". For higher resolution resource packs, "up_center" and "down_center" may also be relevant but I don't personally plan on using these.