Remote Buddy, in fact, uses the Finder as well to put your computer to sleep. It uses this AppleScript:

tell application "Finder" to sleep 
(the Finder "sleep" command is documented by Apple as "Put the computer to sleep")

Remote Buddy has no influence on and does not change your settings regarding wake on lan. This setting resides in System Preferences > Energy Saving and is not touched by Remote Buddy in any way. Remote Buddy has no code in that area.

Regarding wake by Apple Remote, please check your Apple Remote pairing settings. If you have paired an Apple Remote to your Mac, it'll only wake up on a button press of that remote. This is a hardware feature of the Apple IR Receiver and can't be changed or extended by Remote Buddy.

Depending on your settings in Remote Buddy, however, you can use more than the one paired Apple Remote while your Mac is awake.

Unpairing the paired remote in Remote Buddy > Hardware > Built-in Receiver, System Preferences > Candelair or System Preferences > Security may be worth a try.

Best regards, 
Felix Schwarz