Dear Jaybee,
In the current plug-in version you cannot exclude root files from the file date/size monitor, as you correctly noticed. Achieving this, is a bit more complicated than throwing in a few lines of additional code. As such, the idea to exclude root files from the date/size monitor is a good one, but its implementation must be done with care. We'll put it on the wish list for the next version of the plug-in.
Until then, you may consider transferring your log file to a root folder, for example the existing '/logs' or a new '/mylogs' and configure your Joomla! or the extension to write to this folder (global config or otherwise). Next, exclude this folder from the date/size monitor and you're done.