Renaming a .desktop file renames the file but pcmanfm-qt displays the name inside the .desktop file.
is there a setting to always display the filename?
I also won’t let me move it into a directory that has a *.desktop entry with a different name but the same Name in the desktop entry (it looks like what is happening).
About your first point. I once had the same desire. I am not a specialist on pcmanfm-qt’s desktop ‘engine’, and you should probably post your question(s) at the lxqt-project.org website (try one of the Instant Messaging channels there).
My work-around was to use the fields Name and GenericName to discriminate between different versions, locations etc. of a program. That worked for me.
The second point seems to me as by design.
If it really hinders you, you can always have a look at the code (same website as I mentioned already). If feasible, make your own dedicated option-switches and implementation, and do a pull request to the maintainers.