Here's what I'm currently using to work around this limitation:
Say you depend on external libraries (such as Bootstrap, etc. - F# is surprisingly good at web stuff, too) that do organize their files into folder hierarchies that happen to have duplicate folder names.
You can preserve that folder structure if you change the capitalization of folders that have the same name.
For example, this works (and you can extend this pattern, should the folder name allow for sufficient capitalization combinations)
The following folder structure:
fonts\bootstrap...
stylesheets\bootstrap...
javascripts\bootstrap...
Can be included in an F# project like so (the Content tag is just an example, it can be None , etc.):
<Content Include="fonts\bootstrap\glyphicons-halflings-regular.eot" />
...
<Content Include="javascripts\Bootstrap\affix.js" />
...
<Content Include="stylesheets\BOotstrap\_alerts.scss" />
...
...and so on.
The relevant bit in the above sample: bootstrap vs. Bootstrap vs. BOotstrap.
Everything works after that. I suppose it doesn't work well on case-sensitive file systems unless you muck with actual folder names as well.