"a departure from conventional wisdom; re the large water changes. How big? 25%?"
50%,I'll do more, up to 70% in some cases.
It takes the same time to do little almost as it takes to do a lot.
A number of well respected reef folks also did this every so often and mentioned it really help their tanks etc even on 10,000gal tanks etc.
"Neither skimmer nor carbon will remove phosphates (or nitrates, directly) - again, I'm curious about what impact the bigger bursts of nutrient poor water might have."
I add PO4, I use monobasic potassium phosphate, but you can use H3PO4 andor Fleet enemas(Sodium phophate mainly).
PO4 although is often blamed for many issues, is not the evil doer many ascribe it to with macro's and plants. They love the stuff. Smaller algae tend to do better at lower levels of PO4/NO3 etc.
You will have a rough time limiting algae by reducing PO4.
The small zooxanthllae sort of fall into this group and small nusiance algae fit into this group but the macro's need more PO4 and other nutrients.
"I imagine the conventional "small" changes advice is to minimally impact the amount of plankton in the water column?"
I don't really focus on plankton, I'm after the plants/macro's not the critters and their food. You can add plankton back and culture it in 2 liter jugs etc.
"And, maybe to minimize small differences in pH, temp, etc.???"
No. The pH/Temp in the make up water is very close.
" Not really sure... Since most of the bacterial filter is in the rocks and sand, I don't think it would have any profound impact on that."
I think the lion's share of the bacteria is in the sand, not the rocks. The plants short circuit the cycle, they are the "filter".
Happy plants= happy tank=happy fish.
Take care of the plants and everything else falls into place.
For the filter feeding corals, the plankton and the plankton's food(Both zooplankton and phytoplankton) can be raised separately and doses as needed.
You can also dose this in the between cycles so that less gets into the refuge etc.
I'm mainly a plant/mcro algae person. Ilike refuges as they are and as a tank speciality in themselves. Plants doing the work of filtration, PO$/NO4 etc removal. They are good at it. Much better than any PO4 remover/NO3 remover etc and it's awful hard to seel the old spent PO4 remover wereas I get a fair price for for macro's and plants.
"Well, You're making me think about stuff I haven't really thought about before!!!"
Sorry, I'll try not to let it happen again