As you know, Mexico and Costa Rica will participate in the Copa America as guests. They won't be sending full strength squads however.
FMF's website uses the term "Selection Sub-22" for their team. Same thing for Costa Rica: they will send their "Seleccion Preolimpica" to the Copa America.
FIFA have recently removed Mexico's pre-Copa America friendlies from their list of results. However, the Copa America matches involving Mexico and Costa Rica are still on FIFA.com.
When Côte d'Ivoire sent their CHAN team to the 2010 CECAFA Cup, their matches weren't included in the FIFA Ranking. Same for South Africa (Developmental XI) and Angola (U-20) in the 2008 and 2009 COSAFA Cup.
So I assume FIFA are including Mexico's and Costa Rica's games because Copa America is a continental championship, while the CECAFA and COSAFA cups are only regional tournaments of little international importance.