Well, it can't hurt to try contacting them. I have had good luck -- even with surprisingly-major players -- in reporting problems. As long as you write it up thoroughly and succinctly, and descibe the problem from their point of view, good results can often be had... even a direct response from someone who can/will fix the problem, occasionally. I write up problem reports as factually as I can, provide links to relevant references and URLs, and invite them to look at my files (e.g. to verify that my robots.txt is valid), and generally go with the attitude of "Heads up - I think you have a problem and here is what the problem is."
There is a practical difference between using robots.txt and using on-page meta robots tags. If only the on-page robots tag is used, then the robot has to actually fetch the page to read it. If a page is disallowed by robots.txt, then it (usually) won't be fetched; This decision should be made with bandwidth in mind.
Long-term, the site should be modified to group pages into directories and subdirectories based upon whether you want them indexed. It is just one of many factors that determine the directory architecture of a site, but it can be important.
I took your initial post "X hundred to Y thousand bytes" to hint that your robots.txt was 500 to maybe 99kB in size, but big is a relative term. So, is it 38,357 bytes, or 38,357k bytes? Either way, it's big, but 38,357k bytes (37.5M) is huge!