I just realized that the Grep for ID storage does not contain a lookup range?

Ah, I see what you are running into here. You are looking at an InDesign Find/Change Query (.xml) export and wondering why there is no scope specified like document or article?

You are correct in thinking that the scope of where a GREP query runs (document vs selection vs story vs article) is not stored in the .xml file of the Find/Change Query. That is not a bug, that is simply how InDesign’s Find/Change system works. The query stores what to find, how to find it, and replace settings, but not where to run it.

I realised this with Find Forwards and Find Backwards is not stored, frustrating. 

The scope is chosen at run time by you, in the Find/Change panel or by the script or UI you are using.

app.activeDocument.changeGrepPreferences = NothingEnum.NOTHING;
app.activeDocument.findGrepPreferences = NothingEnum.NOTHING;
app.activeDocument.findGrepPreferences.findWhat = "(?<=m|M)(2|3)(?!\\d)";
app.activeDocument.changeGrepPreferences.appliedCharacterStyle = app.activeDocument.characterStyles.itemByName("superscript");

app.activeDocument.changeGrep();

In this example, the scope is the whole document, defined by app.activeDocument.

I think this is correct for just selection

app.selection[0].changeGrep();

You are not wrong. The XML does not and cannot define scope.

The scope is defined at runtime. As far as I know there is no way to embed a scope (Document, Story, Article) into the .xml query file.