It might have been better if I had phrased (2) a little more strongly like Carroll did: something like 'the physics of everyday life is completely understood' or 'there will be no practical applications of physics beyond our current theories (the standard model and general relativity)'.
Yes they might be compatible. But if (2) is true, then the discoveries of (1) quickly become irrelevant. This is what Horgan is getting at. If new theoretical ideas don't have any practical implications for our corner of the milky way galaxy, it is going to become very very hard to keep up a never ending sequence of experimentally confirmed discoveries.
Note that Carroll was not claiming that Newtonian mechanics explained all of everyday life. He was claiming that the standard model plus general relativity contained all of everyday life. The analogy to Newtonian mechanics is to help people see how little impact on everyday engineering practice even the discovery of quantum mechanics had (and QM is a hugely practical theory that explains materials, semi-conductors, etc as you note). My guess is that the quantitative discrepancies between current predictions and measurements leave little hope that discoveries beyond the standard model and GR are going to have any practical applications except maybe in the distant future if we need 15 digits in the magnetic dipole moment of the muon or are trying to travel outside our galaxy or are considering the heat death of the universe. Like Horgan, I would love to be wrong. But I just haven't heard any good empirical arguments to support claim (1) that are deeper than 'past performance predicts future results' mixed up with wishful thinking.
The mercury/Vulcan reference is an interesting one. Note that the precession of Mercury is a pretty small effect and the GR effects that produce it have only recently begun to have practical applications in the global positioning system clocks. Do you have modern candidates to propose where unobserved entities are hypothesized to patch up measurements with the standard model or GR? Dark matter and Dark energy are the obvious candidates. The Higgs particle also could have been such a thing. If it had not been observed we might have needed a paradigm shift, but even that probably would not have made much practical difference. You don't need to be able to predict the masses of the particles in the standard model for practical purposes. It works quite well to measure their properties and use that to predict how they behave.
A 19th century analogy is to chemistry. Chemists in the late 19th century were able to put in place much of modern chemistry without having correct ideas about how a chemical bond actually worked. Quantum physics did not replace chemistry. It mostly explained things that were already known. But it did something else...it suggested where to look for new discoveries: the addition of Hafnium to the periodic table for example. It also opened up precision calculations of bond energies, bond lengths, etc which have been quite useful. That is what happened when we finally figured out how ordinary matter works...the stuff we are made of. (1) is a guess that figuring out what dark matter is or the properties of possible non standard model particles formed at energies above 100GeV will guide us to new areas of inquiry that lead to breakthroughs and practical applications. But it seems an unsupported guess. We already have discoveries like the top quarks and tau neutrino that didn't lead to any significant breakthroughs or new technology. Does anyone have any dark matter hypotheses for which they have a potential application? It is just very hard to imagine what one could do with a source of gravitational force that interacts so weakly with ordinary matter than it is currently only detectable on length scales of an entire galaxy. And dark energy is much much farther from engineering use.
So let's keep trying to find new breakthroughs. But it is also good to be honest with ourselves about what we have reasons to expect and what is wishful thinking.