off-hand, from what you type, it seems that your keybinding is not working because the program is not actually in your PATH - your PATH has /home/user/bin - i suspect if you `ls /home/user/bin` you do not see an executable named 'icecat' - if you did, that would probably be incorrect anyways, because the icecat program needs access to entire directory tree that it ships with - so you probably have that directory under your /home/user/bin which mean you need to change your keybinding to include the directory name - note that there is no need for icecat to be in the PATH if the only way you will ever launch it is with that keybinding - just set the keybinding to /home/user/bin/icecat-52.1.0.en-US.linux-x86_64/icecat or whatever is the appropriate path - also note the the %U plays no role for a keybinding - that probably came from a .desktop file where it is a placeholder for a URL parameter
the 'default' GUI link click-handler is trickier - i am not certain how it works myself - some GUI programs on my system open links in iceweasel and others in netsurf but ive never bothered to investigate why - i suspect some program refer to whatever is in /etc/alternatives/ as with by `update-alternatives` and others may pass the link to `xdg-open`
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