Sounds like your concerns ...

Sounds like your concerns are driven by conflicting information.

1st some municipalities add ammonia with chlorine to create chloroamines to get extended distances of oxidant in the service lines of their potable water. At least one water treatment company is promoting adding ammonia to create chloroamines in the recirculating water. Chloroamines are very toxic. The issue in cooling towers is centered around copper alloy corrosion due to the ammonium ion. Adding Bromine creates a more toxic bromoamine but the copper issue remains.

Chlorine dioxide is easily consumed by all forms of other materials decreasing its availability to kill biological materials. You do not want to add it as you would in a typical replacement of chlorine gas or bleach.

There are a number of ways in which you can generate ClO2. Some will really increase Cl levels and other will not. Both methods will lower pH so if you use acid for pH control going the Purate route will be the most economical and will have the lowest chloride production in the water.

Do not expect miracles from ClO2. It can do an excellent job on algal materials but not if you do not have contact with a sufficient concentration.  

Loss thru the cooling tower is well overrated. What usually happens is the ClO2 goes after a bunch of organic material that has built up in the CT fill. This is actually a good thing. The bad thing is you get no residual in the basin where you want to kill the alga. 

There are great benefits to ClO2 but it is not a cure-all.

The greatest mistake made is not identifying what "your" problem is and what are the best solutions for "your" problem specifically.

Hope it helps.