there never would have been all those deep incised plunge pools the structures mimic
I agree with doing REAL restoration, rather than "stream carpentry." Reconnecting streams to their floodplains, removing constraints to channel movement, restoring normal amounts of large woody debris, all that good stuff.
But doing so will result in formation of deep pools. Deep pools are formed by natural processes. Including plunge pools, formed where the water drops over large woody debris creating deep plunge pools. And pools are formed at the outsides of meander bends. And confluence pools are formed where secondary channels rejoin the main channels.
In similar streams where some degree of natural stream/floodplain structure and functioning exists, I've seen many pools that are 3 feet deep, and some that are 4 feet deep or more. It is normal for these types of streams to form such pools.
Many people think that freestone streams are "naturally shallow." They're WRONG, to put it plainly. The reason they think that's normal is because it so common for these streams to be dominated by shallow habitat. But it's so common because the streams have been so highly altered, in ways that inhibit pool-forming processes.
If these streams were restored in the ways that you propose, I totally agree with that. But just understand that that will result in large, deep pools with lots of overhead cover. That would result in the streams supporting a high biomass of trout, bringing it up closer to what existed pre-disturbance.
In mixed population streams, the brown trout will dominate the best holding water i.e. the places with the highest quality pools and cover. We all know that.
But real restoration would not only create large pools, it would also create a wide range of complex habitat. This would include smaller pools, pocket-water, shallow water with heavy cover, multiple channels, beaver dams, etc. Much of this habitat would benefit brook trout.
In streams that hold only brook trout, the most biomass of brook trout and the largest individuals are in the best holding water, where there are pools and overhead cover. The large deep pools and good overhead cover are very beneficial to the brook trout populations in these streams.
On much of the freestone brook trout stream mileage the difference between the stream supporting 10 kg/ha and 60 kg/ha of brook trout comes down to holding water, i.e. DEPTH AND COVER.
There is a NC PA brookie stream that I've fished a fair bit. The PFBC rates it as Class C, which is quite low. Their report says it's an infertile freestone stream. But that is not why it has such a low population. Most of the stream has very shallow habitat. Not for natural reasons, it's from man-made disturbances. But there is one section, only about 1/3 mile long, that has quite good habitat. And that section is loaded with brook trout, including nice ones of 8-9 inches. If they surveyed just that section it would surely be Class A. There is nothing wrong with the water quality. There are decent numbers of aquatic insects. The difference is the physical habitat.
One of the best ways to realize the extreme importance of pool habitat is to walk small freestone streams during severe droughts. Often the pools are the only place with water. The stretches between the pools are dry. The only place they can survive the drought is in the pools.