ok let me give this a shot... lol
Now I am no expert on water chemistry so hopefully someone who is will chime in.
I am not sure that alkalinity and ph are directly related. Although I am sure they will influence each other, you can have an alk of 12 and a ph of 8.3 or your alk can be 7 at the same ph... But like I said, I am pretty sure that alkalinity can affect ph but not sure how so...
Now to answer your question... The reason you want such a high Alkalinity in your effluent is that is how much calc/alk your ADDING to your system... Ok I don't know really how to word this so let's start from the beginning. Water comes into the reactor at your current parameters (i.e. 8dkh and lets say PH of 8.35). Then CO2 is injected into the reactor which then LOWERS the PH to essentially what it is coming out at (i.e. 6.7). This makes the water more acidic allowing it to dissolve the media which drives up your calcium/alk of the water in the reactor (the effluent). Then it is dripped out at super high calc/alk levels (i.e. 25-35dkh) and the calc and alk are slowly added to your system (hopefully at the same rate they are being used up by your corals, fish, coraline algae, etc..).
Your right, you should be worried about driving up your alk too much or too quick so if your system is stable then leave it be! The only reason to up your effluent alk is to increase the amount of calc/alk being delivered to your system. In order to do this, you can lower the ph in the reactor which will dissolve MORE media and raise the amount of dissolved calc/alk, if you want to lower your alk then raise the ph in the reactor, this will decrease the amount of media being dissolved and in turn lower the amount of dissolved calc/alk in your effluent. Either way you should shoot for a STABLE TANK alk. If your reactor is keeping everything stable and you wish to increase alk or calcium levels, do so with alternative buffers (i.e. 2 part dosing)
I hope that makes sense... I was just kinda rambling..
Chevegan - From what I read, although the effluent is coming out at a lower ph, when the calc/alk are dissolved into the system and it stableizes, it will actually work as a buffer to INCREASE PH... ??? Don't know how or why, but that's what they say... go figure...