On top of the cited rules there is a Commission Decision benefiting third-country ICAO IR holders. See annex V in 2014/69/EU: Commission Decision of 6 February 2014, etc,
EUR-Lex - 32014D0069 - EN - EUR-Lex
Para 3 in section 2.2 gives a wordy summary:
The Agency agrees with the reasoning provided by the UK. The rule [FCL.625(d)] does not take into account the possibility that the licence holder may have been flying under IFR using an IR held on a 3rd country licence during the 7-year period which has been renewed during that period and which is therefore valid. The intended derogation would concern holders of licences in accordance with Part-FCL that include the ICAO compliant IR. If such pilots after a certain time stop to fly on that licence but continue to fly on an ICAO based third country licence that includes an IR and would request then to renew their IR on the European licence they would only have to fulfil the revalidation criteria contained in FCL.625(b) based on the current and valid third country IR. This means that the rating holder must pass the proficiency check, but will not be required to undergo training or to re-take the theoretical knowledge examinations. In the case of a pilot who held a third country IR that is not any longer valid but has been revalidated or renewed within the preceding 7 years the rating holder shall comply with the renewal requirements in FCL.625(c), but will also not be required to re-take the theoretical knowledge examinations. The Agency considers that this provides a level of safety equivalent to that provided by Part-FCL.
See also Commission Decision of 1 July 2014 (2014/425/EU), etc,
EUR-Lex - 32014D0425 - EN - EUR-Lex
As far as I'm aware FCL.025(c)(2) will still apply, i.e. ATPL exam credit for the granting of an ATPL will expire 7 years after the last validity date of an IR entered in the Part-FCL licence.