The normal reason they resort to combo codes is to combine two existing setup codes to work one device. This is common for receivers. Basically, a receiver is a preamp/amp with a am/fm tuner added. So by combining the two seperate existing codes, they can access the functions for both parts of the receiver with one "new" setup code. With the rash of dvd/vcr units being released lately you'll likely see this more and more. Same with HT's in a box; except it get's even more complex.
The drawback, besides making advance codes without JP-1 unusable, is you may lose some functions, there's only so many buttons on a remote, or it'd require a remote almost as long as a baseball bat. Thus, more functions go from being discretes to being toggles. The firmware may support the discretes, but the dilemna now, if you can find them is having buttons left to assign them to. In many cases it means choosing other functions you'll have to delete.
One avenue is to use shift-buttons, effectively double-upping buttons. That requires pressing 2 buttons ("shift"=P, magic, set, setup, code search) and the button assigned to unless they are the numeral buttons which requires a double press of the "shift" button. But then if it's a combo code, this is only possible with JP-1. JP-1 allows more flexibility and you may not even want to go these other "kludge" routes since there are other tools available; device multi-plexor, device combiner, and others(depending on remote "family").
Jim