Can I compare only file contents?

I would have thought that WinMerge with the following settings would work:

If it doesn't, I would ask the question in their forums.
I believe this is worth the effort, as WinMerge is my best file-compare product.

Try setting the Compare option "Ignore carriage return differences".

Differences in line endings (CRLF/CR/LF) are the usual suspect when one mode of comparison (binary) reports differences but another mode (text) claims that the files are the same.

Try with the software called 'Beyond Compare'.

I had the same problem with WinMerge 2.14. So I tried WinMerge 2.16.2, problem solved.