OK, chemistry time.
Your statement is true, that hydroxide addition impacts all other alkalinity contributors, but it is also true of carbonate addition. Not all of the carbonate you add stays as carbonate.
There is absolutely ZERO difference in any chemical in the tank whether you raise alkalinity and pH using hydroxide or carbonate, once you are at the same pH and alk.
All of the alk contributing ions are in an equilibrium with one another where the concentration of each one is only dependent on the pH and alkalinity, regardless of how you got there. If you know the alk and pH of seawater, you can calculate the concentration of borate/boric acid, carbonate/bicarbonate/carbonic acid, and every other alk contributor no matter what the history of the water was in relation to adding hydroxide, carbonate, or bicarbonate.
I could write a large number of acid/base reactions that happen almost instantly, but these few give an idea of what happens after addition of any acid or base:
OH- + B(OH)3 --> B(OH)4-
CO3-- + B(OH)3 + H2O --> B(OH)4- + HCO3-
OH- + CO2 --> HCO3-
CO3-- + CO2 --> 2 HCO3-
OH- + HCO3- --> 2 CO3--
CO3-- + HCO3- --> HCO3- + CO3--
Note that if you add carbonate, this reaction is actually the dominant thing that happens to the added carboanae (unless the pH is above about 8.9 where more of it stays as carbonate)
. At pH 8, only about 11% of the added carbonate stays as carbonate. Almost all of it is converted into bicarbonate:
CO3-- + H+ --> HCO3-
You can see from these sorts of reactions that while hydroxide does react with boric acid to form borate, carbonate also reacts with it to form borate. The amount of borate only depends on the final pH since this equilibrium between boric acid and borate always holds to a fixed equilibrium, and the ratio of boric acid to borate only depends on H+ (pH):
B(OH)4- + H+ <---> B(OH)3 + H2O
On the organic acids idea, this seems to me to be largely an idea driven by marketing folks who don't understand chemistry, and want to sell products to defeat this imagined enemy. There are very, very few organic acids in a reef tank that are not almost fully in the anion form at pH 8. Most (like acetic acid) have a pKa around 5, so that only 0.1% of them would be in the acid form at pH 8.
Nevertheless, the carbonate and hydroxide additions both impact those small number of organic acids:
OH- + RCO2H (an organic acid) --> RCO2- (an organic anion) + H2O
CO3--- + RCO2H (an organic acid) --> RCO2- (an organic anion) + HCO3-
It certainly is true that adding organic acids can drop the pH and partly drop the alk of tank water (since only a portion of the organic acid is titrated in a total alk titration), but such acids do not play an ongoing role in lowering pH.
Hope this helps folks understand that adding hydroxide does not introduce any long term issues.