Hard to say - FIFA (website updates) don't always get info from the relevant department (match authorisation) on time, or sometimes only on request (so if they are told about a possible unauthorised/B match, they might then ask the match authorisation team about it).
Slovakia wrote to FIFA before the matches were played, however. So did Slovenia and Finland. And apparently, Ivory Coast-Uganda today was also not an A-match for similar reasons (not sure which of the 2 teams didn't want this as an A match).
Croatia didn't write to FIFA with any special instructions, and so they are classed as A matches.
I don't think it's healthy to have individual FAs in charge of what matches they want to be classed as A matches. It opens the ranking up to manipulation (even more than it already is).
Might be a bit simplistic, but surely there should just be some kind of registration deadline to call the upcoming match an A or a B fixture. If the friendly is outside of the international break, both teams have to agree that it is an A before it is played otherwise it is B, if it is in the break, both teams have to agree to it being a B match or else it is deemed an A, which should prevent any attempted gaming of the rankings system from big nations trying to dismiss the result.
The technicalities after those guidelines regarding disagreements or fixtures arranged post-deadline are something that a group of people in Zurich are paid to deal with.