If you change configuration options in the 'Site -> Customize Viewers' section, then they will apply to all galleries in the current theme. (Otherwise, if you just want to change configuration options for a specific gallery, you can do so by editing the gallery's own page.)
Either way, just be sure to click 'Update' and 'Publish' after making any changes.
I have just double-checked and the imagePadding is working fine when changed in the 'Site -> Customize Viewers' section. Please note that the imagePadding is applied to all sized of the image (not just the bottom).
Also, it should not be necessary but if you are not seeing the changes you make, try clearing your browser's cache before reloading your gallery's web page.