This is documentation of names in various languages for various geographic regions. In 2007, they opted to document in some cases (but not all) the language in which names are expressed using ISO 639-1. There's no indication given that this was not sufficient for their needs at the time. There are clearly cases (like entries for South Africa) where they did not list an ISO 639-1 ID because it doesn't exist - and that doesn't appear to have hindered their purpose in any way.
However, if they were to state (which to my knowledge has not happened) that they wanted to include alpha-2 IDs in cases in which one was not available, that would still not necessarily imply a sufficient justification to add new alpha-2 IDs. Note that this document isn't a protocol for public data interchange; they are simply providing information, and as a convenience to some readers have in some cases provided the ISO 639-1 ID.
But even if they came saying they'd like to use IDs in some protocol for information interchange, that still doesn't necessarily imply a requirement for support using alpha-2 IDs since we have standard alpha-3 IDs that can be used for that purpose. It would be somewhat comparable to the Central Bank of Russia, which has just recently adopted a new symbol for the ruble currency, asking for character encodings to support the symbol: it will NOT be supported in ISO 8859-5, but it isn't needed in ISO 8859-5 since it WILL be supported in ISO 10646.
All you have really done is show that someone has used ISO 639-1. But we already knew it had been used.
From: ISO 639 Joint Advisory Committee [mailto:[log in to unmask]] On Behalf Of Gérard Lang-Marconnet
Sent: April 14, 2014 6:29 AM
To: [log in to unmask]
Subject: UNGEGN List of Country Names (2007)
You will find thereafter an official UN document, edited by the UNGEGN, as preparation for its M87 publication in 2007, also using alpha-2 code elements to represent "national official languages" recognized in the UN member states. You can verify that India and South Africa have lists in conformity with ISO 3166-1, and that Comoros uses Shikomor.