To understand Va you need to remember there is the design Va speed and the Va as placarded in the flight manual etc. The latter must be less than or equal to the design Va. The pilot only knows the latter. Va1 and Va2 are only relevant to the designer.
Va on the 25.333 is the design limit just referred to for which the aircraft structure must be designed to withstand loads associated with certian manoeuvres eg rolling as per 25.349(a)(2). (Roll rates are faster at slow speed)
Now Va1 and Va2 in 25.333 are related to the manouevre pitching accelerations (ref 25.331(c)(2)(i) &(ii)). tailplane loads etc must be etsblished for points on the line A2 to D2 in 25.333 - note this includes point A as well. Remember that Va in the FM is an upper limit (usually placarded as "do not make abrupt manoeuvres above this speed").
The designer however has to design for pitch accelerations throughout the flight speed range: The lower the speed - the higher the required pitching acceleration for design purposes (ref the equation of 25.331(c)(2)(i) &(ii)). Hence speeds less than Va may result in the highest tailplane loads etc.
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