The bottom input panel — whether from find and replace or a plugin (such as Advanced New File) — is partially obscured and difficult to use when line_padding_bottom and line_padding_top are set. In my case I have the both set to 6.
Perhaps line_padding_* shouldn’t effect UI input — or perhaps there should be separate settings for code and UI?
good news - there are 
if you create a file called Widget.sublime-settings in your Packages/User folder, you can set
{
"line_padding_top": 0,
"line_padding_bottom": 0
}
which will override those settings for the text boxes in the find/replace panel and the input panel etc.
Note that there is no need for any UI textboxes to be obscured, just resize the panels using the mouse.