While it is true that the in the novel Vin assumes that it is an external version of Gold we are told later on in the series rather explicitly that this is not true. In fact, Gold and Atium are strange pairing in a number of different respects, not the least of which is that one uses the base metal to see the past while the other uses the base metal to see the future.

In fact, when Vin burns Malatium and looks at the Lord Ruler, what we see is the following.

And then she saw him. Another man, standing right beside the Lord Ruler. Where had he come from?

Initially, she sees only one man. If we assume that Malatium works like Atium, then this makes sense. Much as an individual only has one future when Atium is burned, an individual only has one past.

So, per your question that leaves the concern of where the second Malatium shadow enters into it? If we look forward a couple paragraphs we see the context for this second figure. (I've added emphasis based on how I read and interpreted it.)

Vin turned to the side. There was another unfamiliar man beside her, a young nobleman.

Vin has turned to the side. Why would she need to do this before seeing a second image of the Lord Ruler and why would it appear next to her and not him? So, it doesn't make much sense that this second Malatium shadow is of the Lord Ruler. So why would she see a second Malatium shadow at all? Consider that when one burns Atium it allows one to see all the Atium shadows in one's field of vision (including the Atium shadows of people one is not looking at directly, as evidenced during various fight scenes in the later books).

So if not the Lord Ruler, who else could cast that Malatium shadow? Who would be close enough to cast a shadow beside her but not be directly in her field of vision? If we back up a few paragraphs we get an answer to that to.

The Inquisitor pinned her arms to her sides, however, and backward kicking did very little good.

There is an Inquisitor standing directly behind her. If he cast a Malatium shadow it would appear beside him which is beside and behind her. So if she turns her head in the proper direction, she would be able to see it even if she could not see the Inquisitor himself and it would for all reasonable purposes be described as "beside" her.

This would neatly explain why later on, she only sees one Malatium shadow. When she uses the metal against the Lord Ruler the second time, they are initially alone. This, of course, brings a new question into play. Why would Sanderson include such a detail if it wasn't meaningful to the book? Well, if you look at the way he writes, especially during the last book, in many ways his foreshadowing act much like clues in a mystery novel, slowly guiding us toward the conclusion. By giving out this tidbit about the Inquisitor's past, Sanderson clues us in to the Inquisitors' human origins before they are explicitly revealed.

While it is true that the in the novel Vin assumes that it is an external version of Gold we are told later on in the series rather explicitly that this is not true. In fact, Gold and Atium are strange pairing in a number of different respects, not the least of which is that one uses the base metal to see the past while the other uses the base metal to see the future.

In fact, when Vin burns Malatium and looks at the Lord Ruler, what we see is the following.

And then she saw him. Another man, standing right beside the Lord Ruler. Where had he come from?

Initially, she sees only one man. If we assume that Malatium works like Atium, then this makes sense. Much as an individual only has one future when Atium is burned, an individual only has one past.

So, per your question that leaves the concern of where the second Malatium shadow enters into it? If we look forward a couple paragraphs we see the context for this second figure. (I've added emphasis based on how I read and interpreted it.)

Vin turned to the side. There was another unfamiliar man beside her, a young nobleman.

Vin has turned to the side. Why would she need to do this before seeing a second image of the Lord Ruler and why would it appear next to her and not him? So, it doesn't make much sense that this second Malatium shadow is of the Lord Ruler. So why would she see a second Malatium shadow at all? Consider that when one burns Atium it allows one to see all the Atium shadows in one's field of vision (including the Atium shadows of people one is not looking at directly, as evidenced during various fight scenes in the later books).

So if not the Lord Ruler, who else could cast that Malatium shadow? Who would be close enough to cast a shadow beside her but not be directly in her field of vision? If we back up a few paragraphs we get an answer to that to.

The Inquisitor pinned her arms to her sides, however, and backward kicking did very little good.

There is an Inquisitor standing directly behind her. If he cast a Malatium shadow it would appear beside him which is beside and behind her. So if she turns her head in the proper direction, she would be able to see it even if she could not see the Inquisitor himself and it would for all reasonable purposes be described as "beside" her.

This would neatly explain why later on, she only sees one Malatium shadow. When she uses the metal against the Lord Ruler the second time, they are initially alone. This, of course, brings a new question into play. Why would Sanderson include such a detail if it wasn't meaningful to the book? Well, if you look at the way he writes, especially during the last book, in many ways his foreshadowings act much like clues in a mystery novel, slowly guiding us toward the conclusion. By giving out this tidbit about the Inquisitor's past, Sanderson clues us in to the Inquisitors' human origins before they are explicitly revealed.