Their upfront costs are probably nominally higher than average, but state of the art manufacturing moves fast, the up front costs are either paid back quickly or a waste.
The same forces limit the long term potential; if they don't keep up, the investment quickly withers.
Take chip fab for example: 45nm chips appeared around 2008, and cutting edge today is 5nm. Yet something like an arduino may come in around 200nm, the Pi 4 is still 28nm. So there's a fairly long lifespan for manufacturing facilities. Some will retool for the latest tech sure, but plenty will simply pivot to a different market niche commensurate with their capabilities.
For examples in power generation, EDF and HydroQuebec are cases where the government, instead of directly or indirectly subsidizing power generation, decided to just run it themselves, and they both have very clean (80% carbon free for EDF, 99.9% for HydroQuebec), and both make a solid profit while selling the electricty at very low costs (for HydroQuebec, the lowest unsubsidized cost in the world, full stop).
We also have a lot of electrical cooperatives and other non-mega-corp electrical providers in the US. All in all, it isn't a great analogy.
how much are we talking about? does it work out to about the same as other fossil fuels, or order(s) of magnitude less? Also, is it possible to mitigate this by burning the vegetation prior to flooding the area?
About 1.3% of all human caused gas emissions, made worse because it is primarily methane.
As for burning first, that only works for new dams, and you need to de extensive excavation to get at the roots as well- depending on the plant, upwards of half of its mass is below the surface.
Biomass decay isn't the only problem; the article also cites downstream algae blooms, which I suspect would be exacerbated by the occasional dredging necessary to keep dams from being blocked by silt.
A direct comparison to coal is tricky, because a lot depends on the type of coal burned and thr type of plant it burns in. Certainly coal isn't a clean source of energy, but it is clear that hydro isn't either.
Moreso, this can be minimized.
In the end, it's clear that hydro, long term, is indeed clean, moreso than a battery+solar solution would be.
Indeed, this is 1.3% going to 0.06%, despite the fact that hydro represents almost 15% of global electricty generation.
C02 produced by biomass varies with moisture content, but is generally on the level of coal per unit of energy. Moister wood produces slightly more, dry seasoned wood slightly less than coal.
The other option is for a very mature industries with inelastic demand where subsidies go directly to pushing down prices. Like with food and fuel.