I started making a minimal repo to accompany the GitHub issue, however I can no longer reproduce the long filename error for generated resources with the latest Hugo on Windows 10.
Sometime within the past year (around September, I think) I ran into this problem a couple of times and I noticed that Hugo appended the file hash to the original filename for generated resources.
Now, as far as I can tell the latest Hugo replaces completely the original filename for generated resources and therefore the behavior I mentioned above no longer occurs.