Afaik, there is no way to auto say yes for the pops up, but you can script it to auto reload remote.ini file.
Code:
on *:START:.timerscriptcheck -o 0 5 scriptcheck 

alias scriptcheck {
  var %t $calc($timer(scriptcheck).delay / 1000), %i 1
  while $script(%i) {
    var %s $v1
    if $calc($ctime - $file(%s).mtime) < %t { .reload -rs $+ %i $qt(%s) }
    inc %i
  }
}

In order to make this works, you need to turn off monitor file changes (In script editor, press alt+O then untick "monitor file changes" option), otherwise you will still get the pops up.