You can use all buttons (except - of course - dedicated remote control hardware power on/off buttons that don't send anything and just control the remote's own electronics - like f.ex. the power button on the Wii Remote) of all supported remotes with Remote Buddy. Please see

http://www.iospirit.com/products/remotebuddy/hardware/

for a complete list (including the usable button count for each remote as part of the respective fact sheet).

The PS3 Harmony Adapter is detected and handled like a real PS3 Remote (of which, all buttons are supported), so that - insofar as a Harmony Remote + PS3 adapter is capable of emulating the original PS3 remote's button codes - you'll be able to map buttons differently. I personally can't recommend using the PS3 Harmony Adapter, though, because it - in hardware - adds a noticable lag to the button presses that the original PS3 remote doesn't have (the original PS3 remote is pretty instant). So if you're looking for a way to add more buttons, the real PS3 remote is probably the way better - and also much more cost-effective - choice.

That aside, I haven't looked into what IR codes the Harmony Remote sends to the PS3 Adapter, but I really doubt that you can use any remote other than a Harmony Remote together with a Harmony PS3 Adapter.

Best regards, 
Felix Schwarz