Some modern plants use super-critical "steam", and the water never really boils. And from room temperature to just below boiling at atmospheric pressures, liquid water expands around 4%, not under 1%.

PWR and BWR reactors are the main operating principle of the reactor - in both cases, water cooling.

No, the PWR and BWR reactors use water/steam as the working fluid. The fact that they also use a secondary cooling water loop as a heat sink for their thermodynamic cycle is a separate issue. I suspect most "modern" non-PWR/BWR reactors would also use water as a cooling source.

The ironic thing about this situation is that the entire problem could be solved (especially for newer reactors) by building cooling towers rather than using rivers for cooling.

Uh, no. Even if I hadn't RTFA I'd know you are wrong. Cooling towers are built to cool the water through evaporation, and said evaporation (and blowdown) of the proposed "closed-loop" cooling system is what TFA was complaining about, since none of the water taken would be returned to the river.
Also, a lot of cooling towers are built precisely to cool the used river water before returning it to the river, so, because of evaporation, they not only return less water to the river than taken, because the river is lower temperature than the typical ambient wet bulb temperature, what they return is warmer than the river (unless you had a really unusually hot river).

However, is there some kind of water shortage problem that we actually need to resolve? Unless we plan to pipeline water from Kansas to Boston I doubt that use of water in the one area has much effect on availability of water in the other.

On the contrary, that has been a huge issue in many parts of the world (California, e.g.) for at least decades.

The biological contaminants are not hard to control, the heavy metals and other industrial contaminants are a much bigger problem.

Worse, I have seen a college educated mechanical engineer take out his calculator, do a little arithmetic on it, and type the results into spreadsheet cells.

To put that in perspective, the current levels are around 339ppm. If you are not good at math, 6000 is more than 10 x 339.

Not to challenge your main point, but current CO2 levels are above 380 ppm and at the present rate of increase, they will be above 400 ppm in a few years. Also, if the levels were above 6,000 ppm, that would cause a lot of serious health problems for people.

In the industrial sector, which is their primary business and one where they have been leading innovation in for decades.

Honeywell is one of the best-known brand names in the controls industry, mostly due to their past dominance. In the last couple of decades they have not been what you could call leading or innovating. (IMHO, anyway)

You are confusing the "lameness" of the patent with the "lameness" of the feature.

Some of the patents include "thermostat is round and can be rotated"

How could have they possibly applied for this patent in 2004, when they've produced round thermostats with rotating setpoint adjustments since just about forever?