I am not very familiar with this, so maybe not understanding fully.
What do you mean by "Due to ver command..."? There is some command that will display the version and the names you mention come from that?
In my opinion it is always better to go with what is displayed on the front cover of any software. There are many examples where the front cover title and what is displayed when running the software are not the same. My opinion is that what takes precedence is what you would see displayed on a store room when buying the software. Others might think otherwise, so probably using best judgement is the best advice.
If cover is not known/available, go with what the software reports. Don't arbitrarily change it because it seems "nicer" or more convenient.
If the software was first named IBM Personal Computer DOS, then IBM DOS, filenames should reflect that difference. Even if it feels silly, it is what the maker used, so we use the same.