The C. briggsae contigs in this region are incomplete and so the entire orthologous C. briggsae operon is not in one contiguous sequence (in the cb25 assembly). Maybe you could look in the new C. briggsae assembly to see how the C. briggsae ortholog looks?
Do you trust the BLAT alignment?
P.S. I assume that this data is only in the Sanger database at the moment as I don’t see this EST alignment on the live or dev sites.
No weird trans-splicing has to have occurred to create this chimera. In operons, polycistronic cDNAs has been observed many times. To make this one, a dicistronic pre-mRNA was probably just spliced strangely to splice out the 3’ end of .14 and the 5’ end of .16. This kind of thing probably happens more frequently when a rare polycistronic pre-mRNA that contains splice sites that are not supposed to see each other is formed.