../configure --disable-shared --enable-unicode
So you didn't specify --with-gtk=2 or 3. If that machine has both gtk+ dev packages installed it will have defaulted to 2. You should be able to find out by doing, in a terminal, wx-config --list
Rereading your original post, I'm not sure what you are trying to do. If you
wanted a gtk+3 wx build, you probably got one. You could then build your program against it and it should run on that machine. It might also run elsewhere, but only if all of the necessary dependencies are available there and API compatible; which they often won't be.
Presumably your program links to wxSQLite. Did you build or install a gtk+3 wxSQLite? If not, that would explain the error message.
So what is the cleanest method to remove wxWidgets 3.0.3
You installed with checkinstall, so iiuc all you need to do to uninstall is 'apt remove <packagename>'