Yes it does speedster.........Ask any Honda or Toyota Dealership.....wouldnt even look in the engine bay (warranty case) when they know its CNGed or its air/oil filter or engine oil is other than HONDA Supplied....
You replace stock tyres with different size or use alloys ....there goes your suspension warranty...
You install key less entry, there goes your central locking warranty (not the whole wiring).....
You install high amp load (like an AMPLIFIER or anything) there goes your electrical system warranty....
Its not like a break down of cases mentioned on customer terms of use.....its just they need an excuse not having to entertain the claim by pointing out errors at your end.....
When i bought Honda....they clearly mentioned that the faults arising from NON-Honda technicians and NON-Honda parts in other areas of the same system (suspension, electrical, engine, transmission) wouldnt be covered in warranty.........