The final airbases including spawnpoints are described in the Slovakia final readme:
http://www.letka13.sk/~indy/readme/slovakia_readme.pdf
There are two more coded airbases - Drazkovce and Muran - but for small AI fighters only, more info in the readme.
Other changes - some cities were finalized (Trencin) and all objects found on railways were removed (in cities Trencin, Liptovsky Hradok). Also texture placements were improved but it does not affects missions.
I think it is safe to create missions with the beta, possible mission adjustments can be quickly done with the final map.