More than one circuit in a fluorescent fixture, OK?
This is fine as long as they can be joined end-to-end, are identified for through-wiring, or are listed and marked as a raceway, as per NEC 410.64.  Just keep in mind that end-to-end joinable luminaires are limited to one branch circuit (that must feed one or more luminaire(s) in the set) in addition to the circuit that is feeding the remaining luminaire(s).


  410.64 Luminaires as Raceways. Luminaires shall not be used as a raceway 
  for circuit conductors unless they comply with 410.64(A), (B), or (C).
  
  (A) Listed. Luminaires listed and marked for use as a raceway shall be 
  permitted to be used as a raceway.
  
  (B) Through-Wiring. Luminaires identified for through-wiring, as permitted 
  by 410.21, shall be permitted to be used as a raceway.
  
  (C) Luminaires Connected Together. Luminaires designed for end-to-end 
  connection to form a continuous assembly, or luminaires connected together by 
  recognized wiring methods, shall be permitted to contain the conductors of a 
  2-wire branch circuit, or one multiwire branch circuit, supplying the 
  connected luminaires and shall not be required to be listed as a raceway. One 
  additional 2-wire branch circuit separately supplying one or more of the 
  connected luminaires shall also be permitted.


Also, in your case, as per 410.21, the luminaire must be identified for through-wiring in its integral junction box:


  Branch-circuit wiring, other than 2-wire or multiwire branch circuits 
  supplying power to luminaires connected together, shall not be passed through 
  an outlet box that is an integral part of a luminaire unless the luminaire is 
  identified for through-wiring.