Review of stg1/CG11566, currently annotated as dicistronic: the current FlyBase transcripts retain an intron that results in a single long (1000-aa) CDS if removed. The merged protein is supported by models in a wide range of diptera. (Gnomon predicted sequence included in related personal communication.)
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Review of CG12688: CG12688 does not look protein-coding. Looking across other Drosophila species, we do have RefSeq coding-models in about a dozen, but most of them are “LOW-QUALITY” with frameshifts and/or internal stop codons, suggesting the CDS isn’t under functional constraint and we’re just getting coding models because D. melanogaster has a protein. In a test annotation, Gnomon generates a longer 11-exon model merged with the upstream  lncRNA:CR45484 . (Gnomon predicted sequence included in related personal communication.)
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Region flanked by CG40813 and CG41562: A test Gnomon annotation generated an array of 21 genes bordered by CG40813 and CG41562 on the two ends. The internal 19 genes aren’t currently annotated in the FlyBase annotation. The region is also filled with repeats, but the esf2-like genes don’t seem to overlap the repeats.