KEGGgraph result difference

[ag1805x]

I was trying to extract a KEGG pathway as an igraph object of the gene-gene and gene-compound interactions. I observed that different functions from KEGGgraph seemingly give different results. The number of nodes and edges obtained from parseKGML2DataFrame is less than parseKGML2Graph. Also, after parseKGML, the statistics display different numbers of nodes and edges. The graph obtained from parseKGML2Graph has some additional genes, which I assume are the islands that do not show up in the data frame. But what about the parseKGML statistics? And why does the parseKGML2Graph contain ontology or the path itself as a node?

Cross-posted with further details on Bioconductor: https://support.bioconductor.org/p/9159835/