A salination plant constructed with the valves and controller near the base will happily assemble into a functional multi-block structure, but will only use the height of the controller when calculating the maximum temperature and liquid capacity.

If the controller is supposed to always be at the top, allowing it to assemble when it's not is misleading, possibly leaving a newer Mekanism user unaware of a significant problem with their equipment setup. In this case the controller should not assemble and begin working unless it is actually located at the top along with the solar arrays.

If the controller is supposed to be installable at any height in the structure like the valves are, then it needs to properly calculate the full height of the plant instead of its own height. Obviously it is detecting the presence of the solar arrays at the top, because it won't assemble without them, so it could just use their height relative to the base instead of the controller's.

I would much prefer the second resolution, since it would allow for more convenient and flexible designs, and the position of the controller really doesn't have any impact on functionality. When you have a full-height salination plant, you're extremely unlikely to be bucketing liquids in and out via the GUI, after all! Being able to place it wherever convenience or the aesthetics of your build dictate would be a nice option.

This is definitely an issue, but as no functionality is broken because of it I'm marking it as low priority. It will most likely be fixed in the v8 update.