They remain as they physically are after reverting, as logic and rule interpretation dictate.
The feature's last sentence specifies that when it ends "the material reverts to its original substance", mentioning no physical deformation at all. Moreover, there is no mention of the temporarily changed material having any unusual properties (such as stone->wood being unable to burn).
Essentially the ability causes a chemical mutation, not a physical one, both when it is used and when it ends. What that means is that the material's form will not be affected, not by the feature's initialization/end at least.
In your particular first example it would be reasonable to describe the wood as burning properly and then the produced ashes turning into powdered stone, as if disintegrated perhaps. The smoke would become heavier and be similar to that grey fog that you see around mines, very thin particles of stones hovering in the air.
The DM would be free to dictate any specifics on such cases as no rule seems to cover them extensively (and it would probably be impossible to do so without lots of complex definitions and phrases not required in a game of fantasy and abstraction).
One could argue that a very popular similar effect, the Flesh to Stone spell, unlike the feature under discussion, does mention how the target retains any physical alterations caused to it while transmuted to stone. I strongly believe that the lack of such a passage from "Minor Alchemy" is not a hint for different behaviour. Rather, it would be more appropriate to assume that the passage specifically exists in Flesh to Stone because it targets creatures which would bring more discussion/confusion upon missing, in comparison to the Minor Alchemy case.
As a final note, I would consider such usages to be rather interesting and creative when it comes to overcoming challenges for the players and would seem rather fitting (theme-wise and as a power level) for the Transmuter subclass. I would advise DMs seeing such applications to not feel intimidated by them but rather welcome them in their story as appropriate.