Many very bright people are absolutely convinced those provisions refer only to license conversions which is a completely different thing (and only relevant to people who want to fly EU-reg planes, typically IFR, but have only an ICAO non-JAA IR). And sure enough that is how it reads, superficially... this may have been intended by EASA because it is not in their interest to make such an aggressive measure too obvious too early on in the process.
Yes having read it again I see what you mean, the tables in the NPA and CRD actually seems to refer to just the conversion of licences issued in the past by EU member states to EASA licences, not non-EU member licences. Leaving as you say a bit of gap in the regs if one wants to go for anything other than the one year validation. The document does cover the conversion of foreign licences, on the last page, but makes not specific mention of IRs.
Watch this space I guess...
The prospect of a bilateral licence agreement sounds interesting though.