Well you need to customise the filelist.tpl file. Instead of using %item-full-url% or %item-url%, you would need to use.... %host%%folder%%item-name%%item-ext%, this should print a full link without the encoding.
However if Macro can be used in the filelist.tpl, there is a one that can remove the uri encoding... But Macro may just confuse you further...
Something like:
[file]
%item-full-url%
to
[file]
%host%%folder%%item-name%%item-ext%
filelist.tpl is separate to the main template, its usually used for other purposes, beside the accessible HFS template.