Ok thanks a lot, I see what was wrong.
In fact I was lauching emulationstation from the .xinitrc file because I wanted to avoid using openbox. But is seem not to be possible. To make it as clean as possible I edited my files like so:
/home/pi/.initrc

exec openbox-session

This will start an openbox session in X and trigger the autostart file that i edited like so:
/home/pi/.config/openbox/autostart

xterm -fg white -bg black emulationstation -fullscreen

This will lauch emulationstation in a black xterm terminal in fullscreen which is used to display the file manager or retropie setup.

@Impman66 said in Is WinSCP or Putty necessary?:

So it begs the question, is WinSCP, Putty, or any other "file sharing" program necessary?

no, there are 3 supported methods of copying roms, and you're simply using the third: https://retropie.org.uk/docs/Transferring-Roms/#samba-shares

Update, I've gotten it semi working. Somethings wrong with my retroarch setup, the default bios directory is not the actual bios folder, i had to manually set it to that. Semi working because I can't seem to get retroarch to use global configs, i have to manually set each systems directory.

But thats not the topic of this thread. I guess for the time being this is a moot issue, the asterix dont seem to mean anything and arent causing the problem. Thank you all for your time.

I wonder if my issue stems from doing an update to retropie 4.4 rather than a clean image?

@pjft

Actually, they don't.

When I transfer via USB, the autocopy feature doesn't duplicate them. They only exist on the stick.

And when I do manual transfers in file manager (of bios or themes), I ignore them, so no sweat.

Okay, it looks like I have it running pretty clean now. Thank you all so much. Next I'll try to figure out how to add Famicom CDS, Super Famicom, Virtual Boy and maybe Game & Watch directories/roms to my build. Time to start hunting through the threads [slaps and rubs hands together in eager excitement] :)