That does make a big difference: a table cannot continue to a page other than the next one (I haven't tried putting a table in a linked text box to see if that works, but then the table wouldn't be necessary).
It's easy to hide an empty text box manually (use the Selection pane and click the "eye" icon next to the box's name), but that doesn't remove/omit the whole page. To do more, you could insert a bookmark that extends from the page break before the continuation
box (which I assume you have in the main merge file to make the box appear on an otherwise empty page) past the paragraph that contains the box's anchor. Then a macro can delete the bookmark's range if the box is empty. That macro would look something like
this:
Sub DeleteContinuationBoxPage()
Dim shp As Shape
Set shp = ActiveDocument.Shapes("continuation")
If Replace(shp.TextFrame.TextRange.Text, vbCr, "") = "" Then
ActiveDocument.Bookmarks("deleteme").Range.Delete
End If
Set shp = Nothing
End Sub
[Note: you can assign a name to a text box in the Selection pane, and the above code assumes the box is named "continuation" and the bookmark is named "deleteme".]
This macro would have to run after the merge and before the save to PDF. Some third-party merge software will let you run a macro of your choice on completion; otherwise you have to remember to do it manually.
The macro can be extended to handle the page reference (an ordinary cross-reference in Word can't show a "N/A" result).