Yes, you're correct. The default palettes are different between the AOZ/PC and Amiga manifests.
This is normal. If you want a program that you write in the Amiga manifest to use the same palette in the AOZ manifest, you can create an include file containing an equivalent palette definition, or you can alter the palette in your code using the Manifest$ function to determine which palette you're working with. If you just duplicate each nybble to make a full byte you should have the same palette. For example:
If Manifest$="amiga"
Palette $000,$FFF,$F00,$0F0,$00F,$FF0,$0FF,$F0F
Else // AOZ/PC manifest
Palette $000000,$FFFFFF,$FF0000,$00FF00,$0000FF,$FFFF00,$00FFFF,$FF00FF
End If
You can also use a percentage with the nybble $F being 100%, and $0 being 0%.
Multiply $FF by the percentage, and you should have your AOZ color.