The Syphon FIlter alternate cover (The one with the flag, etc) was never produced. The inserts on the case were promotional inserts companies sent to stores to use before the game comes out. We get them all the time for the DVD cases, sometimes the exact final insert, barcode and all. Considering the Game was released 2 months after September 11th (almost to the day) I'm sure Sony wanted to avoid any and all possible controversies. See also Spider-Man PSX re-release censoring and MGS2 PS2 censoring.
It's possible someone used the promtional inserts to 'complete' a game. I've done it with N64 games and the cardboard display boxes. If it was a "New" game, than that was quite possibly the only one. Ever.
The Lethal Enforcers was never packaged with the Justifier. The Justifier *did* advertise LE, Area 51, Die Hard, and one other game on its box though. The Japanese version did have Project Horned Owl (the original PSX Light gun game) packaged with the Gun, however.
I don't think the Reel Fishing II rod package was an actual SLUS style release (like Bass Landing was)...I'm pretty sure that was a third party accessory company deal with it. Interact did a similar job with DC Sega Marine Fishing and their DC rod.
Jason