Without being 100% precise in the defintions I will give it a try :-)
for AppID to work the firewall needs to take fragmented packets, keep them in-memory until the entire PDU is received and reassemble them in-memory to figure out which App the packets relates to.
When doing normal L4 firewalling with NAT the reassembly doesn't need to be done on the firewall/router. It just needs to decide if there is a matching session and if NAT-rules needs to be applied. Rreassembly of fragmented packets are handled at the destination where they are handed over to the higher layers in the OSI model.
A reference scheme for the Junos flow module can seen below. It's in the services part that the preprocessing and reassembly happens.
