I do not get any warning when I upload a file with an upper case file extension whose content consists of entirely the same data and therefore calculates to the same SHA1 hash at test.wikipedia.org and it is reported to be the same at commons.wikimedia.org.

This is because MediaWiki looks up the files by {hash}.{file-extension}==fa_storage_key. Since fa_storage_key contains only lower-case file extensions and upper case extension from input are not yet normalized, nothing is found upon uploading files with upper case file extensions. This should be trivial to fix: Look up the SHA1 and not the storage key.