My guess is that these unnamed officials in Spain and France are playing games with terminology, to confuse matters. Like they didn't "refuse airspace", they just refused to give the plane a flight plan through the airspace.
My guess is that the list of countries restricting airspace was said by an Austrian "official" to the Bolivian passengers, including the Bolivian president once they landed. At no point in time I have seen an article stating the "unnamed officials in Spain and France" have closed the airspace to the Bolivian president. What is official is that named French and Spanish officials have denied such statements.
Additionally, the plane has landed in Spain to refuel. No questions asked, no plane searched, no restrictions. This should clear many doubts.
Like you, I can be a cynic, I can read between the lines, I can speculate. When the news stream is limited, and there is a lot of noise, I don't do any of the above.
The real "risk" here is, press and citizens, jumping to false conclusions.
The head of a sovereign state was forced to turn around his plane and land at an airport, then the plane was searched against his will. What false conclusions are you talking about, these are facts, not conclusions.