Hi Chris,
What a great question! When I mark things like this, where something is present in one version but absent in another, I typically only include the tag where some addition is present, and I've found that I don't need to include empty elements for the other version(s). But that doesn't address the question of how to represent the presence of a comma or word in one version and its absence in the other(s). Visualizing in something like Juxta will give you side-by-side correlations of versions, but the designed-for-print output you describe, we'd probably want something like footnotes to indicate variations. 

I'm not sure I understand your suggested output of 
1 , ] *missing* 
If I am following you, in your first example I think you are presenting version A (the lemma with the comma), and do this must be a footnote to line 1. I think what you have makes sense, but it'll only work when there is only one comma in the line. I'd be inclined to include the word preceding the punctuation mark as a rule, even when there's only one comma, just for human readability of the footnotes.

I'd be wary of using the word "missing" to describe the absence of the comma since it implies something like a gap in the reading that needs to be accounted for. I'd be more inclined, I think, to outputting the preceding and following words, with the identifier of the version (in case you're working with versions A, B, C, and D). So rather than "missing", I'd do something like this:

1  version B: now and 

Would that work?

Elisa Beshero-Bondar

Sent from my iPad

On Nov 29, 2015, at 11:39 AM, Chris Forster <[log in to unmask]> wrote:

Hi Folks,

This is not, strictly speaking, a TEI question so much as a question about the conventions of critical editions, but I suspect folks here might have some relevant ideas/experience. If you have an apparatus where a <lem> or a <rdg> is empty, how does one represent it in, for instance, a print apparatus (if transforming, say, to LaTeX)? I'm trying to mark up all differences in a set of poems and often I find that one version has punctuation that another version simply lacks. For instance (this example is entirely invented):

<l>I will arise and go now<app><lem wit="#A">,</lem><rdg wit="#B" /></app> and go to Innisfree</l>

Here the variant reading in B has nothing; in an apparatus how would one represent this? What is the convention? In a print edition (I've been using LaTeX and reledmac, for instance) would it look something like:

1 , ] *missing*

What if it were the base text which had nothing where another witness had something (i.e. the <lem> is empty, but a <rdg> or <rdgs> exist in other witnesses), how would one mark that? (Again, I'm particularly interested in how this is/could be handled in a print/PDF; on the web I've tried, for instance, changing the background color with CSS).

Thanks very much. Best,