Breaking down your original post a bit...
Advantages: You save a LOT of money. A 5-day military park hopper is $312. From Disney, that same ticket is $550-650 for the rest of this year, depending on the specific date. So if you have 4 people, that would be at least $950 saved on tickets alone. There are other advantages, too, like being able to spread the use out throughout the entire use window, and not being tied to any dates. The price is the same for the entire promotional window, too.
For resorts, the availability is limited, and is typically 25% off value resorts, 30% moderates, 35% deluxe.
Disadvantages: Each eligible military members may only purchase 6 salute tickets each year, and must use one for themselves, and show military ID to activate them before the first use. (If you get them from Shades of Green, they are already activated). Also, they cannot be used the last two weeks of December.
Who told you to do that? It's not the way it works. You can't link military tickets "to your cart", if you mean a vacation package. The way it works is that you book the room, with or without a military discount, then purchase the tickets separately, and link them to each individual in
MDE. Typically now when booking with a military discount, the room will be booked as a "basic package". It's just a like a room only reservation, but the deposit is $200, and the balance is due 30 days before check-in. If dining plans return before your visit, you can add that to a basic package.
So you are booking for 5 but only 3 or 4 are going? Sorry, that confuses me. Tickets are not refundable, military or otherwise. It is true that if you book a vacation package including tickets with Disney, that can be modified up to 30 days before checkin, but honestly, I'd try to get firm commitments from the people going on the trip. I personally would not pay so much more only to gain some flexibility.