Hi Kirill,
We have a requirement for a "file" parameter although as you note this isn't really required. I will remove this for the next release so you no longer see the error.
For genbank files the .genome property.txt file is not relevant, as I said there is no property.txt file because a .genome file is not used. The "genome" parameter in this case points to the genbank file. That's all that you should need to do, is that not working correctly?
For fasta based references you do not really need a ".genome" file. You can just supply a link to the fasta file for the "genome" parameter, and one or more annotation tracks as files in the comma delimited list for the file parameter.
In addition to the keys you have listed below there are 2 additional keys, an "alias" file which contains chromosome name aliases, and a "cytoband" file that contains ideogram annotations. These are optional.
The zipped ".genome" format will be replaced in the next IGV release with a json equivalent with more options, basically the structure that igv.js uses. So the ".genome" format is almost deprecated, although backward compatibility will be maintained indefinitely.
Jim