The $20 key from Yamaha has a programmable chip in it, and the blade material is much stronger than the recycled brass china non-chip Yamaha keys, that's why it's more expensive.
For R6/R1 and possibly other bikes with immobilizers here are a few scenarios for replacement keys:
1. I've lost ALL my keys and don't know the original key code (little metal plate that came with your keys when your R6/R1 was new), pick one of the options below:
a) Pay Yamaha $2800CDN and they will give you three new keys, new ecu, new ignition, new gas cap and new trunk lock. You'll have to pick or drill out the existing gas cap and trunk lock and the ignition is very difficult to remove (hardened round head bolts that you usually have to drill out because they are put in with permanent loctite and you can't get a good grip on them being round head).
b) Get your ECU flashed to disable the immobilizer (should be under $100) then have a competent locksmith create a new (non-chip China key) right from the ignition pins. It might not work in your gas cap (the ignition does not contain all of the tumblers of an entire key) so it might need to be drilled out/picked and either get replacement gascap from China which comes with a seperate key or use a keyless gas cap like for track bikes. The trunk lock only has a tumbler or two so usually works fine with created key.
c) Get your ECU flashed to disable the immobilizer (should be under $100) then buy new China ignition and key set from China/Ebay. The ignition will be smaller than your original one (USA style) so you either have to buy a USA triple tree or use some ABS plumbing adapters to take up the space. Usually comes with new gas cap and trunk lock.
2. I've lost my red key and I only have a black one left and want to make a copy:
a) Buy a chip key from Yamaha and take your black key to a competent locksmith that has the equipment to digitally clone the chip of your existing key. The locksmith can not create you a new red key, only clone black keys, so you will need to do this every time you need a key.
b) Dig the chip out of your existing key (check youtube/google for instructions) and tape/glue it (shoe goo works awesome) to the side of your ignition, then get your black key copied/cut (just the teeth) over to a new China no-chip key. You can get red china no-chip keys so you can complete the full set that came with the bike new, one red two blacks, so when selling the bike you can represent you have the full set of original keys (but in actuality they are fake).
c) Get ECU flashed to disable immobilizer and get your black key teeth copied over to a China no-chip key.
3. I have my red key and I want to make a real/original replacement black key.
a) Get a blank chip key from Yamaha. Do NOT get Yamaha to cut the key! Have your locksmith copy the teeth from one of your existing keys (or even better cut a fresh one from the key code you have from the original key code tag) then program the black key yourself using the red key (check youtube).
I think that covers most scenarios for replacement keys for the R6/R1.