the epub generated from that recipe has links that work in the calibre reader, Adobe digital editions and on my SONY PRS 650. Further running flightcrew on it to check its validity pointed to no errors (beyond the usual XHTML guff).
So if the epub isn't working in fbreader, sigil or aldiko you need to open bug reports for those programs.
The cause most likely is the common filenames, as you point out. But a failure to handle files with the same name in different directories is most definitely a bug in the viewer program.
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