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The self-replication assumes also that there is enough energy stored in each planet (or coming from a Sun) to do the work... That is pretty much unlikely.

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And stored in the specific forms the machine can exploit.

Over a long enough timescale, though… really, really slow solar trickle charge to a space-capacitor bank? A thousand years’ suns, culminating in a glorious orgy of smelting?

Unless the capacitor breaks down before it's charged, one of the main problems discussed in the article.

Any chemical bond is a potential source of energy. Plenty of sources of potential energy too able to be converted to work.

That's the source, but for chemical reactions you also need a sink. For instance gasoline is not usable as an energy source without an oxidant. Take away the oxygen in Earth's atmosphere (an asteroid has no atmosphere at all) and now gasoline has no potential energy available. Asteroids have no available oxidants (regolith was already fully oxidized long ago).

If it has been oxidized, there's your oxygen source.

It takes more energy to liberate the oxygen than you could ever get from the fuel. You don't need oxygen atoms, you need the oxidant.

As long as you can get an exogenous reaction from it, which is not guaranteed at all.

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