[RPG] Can a transmuter make silver for his cleric buddy to make holy water

It seems based on a close reading, that there is no volume limit on how much material you can transmute. You are limited by only three factors:

1. It's a single object. The larger the object the more time you have to spend, so you can in theory spend 30 hours converting a small outhouse of 180 cubic feet.
2. The object is all made out of only a single material from the allowed list. If there is any metal in that outhouse, you can't transmute it.
3. You are able to perform the procedure for that long. There might be reason to believe that you can't sustain a single act for more than 24 hours. But perhaps you can.

As long as you are dealing with a single object, made of a single material and you can keep up the procedure, there is no limit to the volume of the object you are transmuting.

[...] you can temporarily alter the physical properties of one nonmagical object, changing it from one substance into another. You perform a special alchemical procedure on one object composed entirely of wood, stone (but not a gem stone), iron, copper, or silver, transforming it into a different one of those materials. [...]
(Page 119 of the Player's Handbook)

Basically you have two possible readings of this description. Either:

1. You perform a procedure. During the performance of this procedure, every 10 minutes, another 1 cubic foot of material gets transmuted into the new substance; 60 minutes after that happens, it turns back to its original form.
2. You perform a procedure. The procedure takes 10 minutes per cubic foot of material. When you finish the procedure, which can take anywhere from 10 minutes to several hours, the entire object transmutes into the new substance.

I think that if the first reading was intended, then the description would include something along the lines of "you can transmute the material at a rate of 10 minutes per cubic foot." I also don't think the rules would be limited to a single object then, but would rather encompass 1 cubic foot of material every 10 minutes, be that 1 object such as a box, or 100 copper coins.

Further, the idea that you can have, say, a "wood" box where half of the box is wood and half of the box is stone, doesn't make much sense. A strict reading of the rules would also make this usage impossible, since once you have transmuted the first cubic foot of material, then the box would be made of two materials and you would no longer be able to perform the procedure!

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.