i would call it a bug, because https://www.w3.org/TR/xml-c14n11/ describes what to do and there is at second top position:

Line breaks normalized to #xA on input, before parsing

in my opinion \r\n should become \n, but what does XmlDsigExcC14NTransform? here we get 
\n

here you can also find a detailed description: https://www.di-mgt.com.au/xmldsig-c14n.html

we change \r\n to \n before we use XmlDsigExcC14NTransform and have no more problems. with our content at least.