Good news, this can be closed! Apparently re-downloading the new SPTInstaller and running again has solved my issues entirely. 
Aside from that, the only thing I changed was running the SPTInstaller.exe from a command prompt in Wine vs using the "Run EXE in Wine prefix" button, which I don't believe made any difference.
I understand linux (Pop OS) is not officially supported, and understand that my unwillingness to install Windows may mean I can't play Tarkov (or SPTarkov for that matter).
That said, currently the automatic installer and the patcher both fail at the same point, which is the window pops up to start patching and then nothing appears to happen. I let the patcher run for ~30 minutes, and the log file showed little activity. So I wrote a quick bash script to apply the Aki_Patches to their original files, utilizing xdelta3 in the same manner that the patcher does (xdelta3 -f -d -s $original_path $patch $original_path.patched), then replaced the original files with patched, and it appears to have mostly worked, though there are some errors indicating bad source files that apparently are preventing it from working. I've tried re-downloading the patches, running integrity check and starting over from the newly copied files, and starting again with a completely new Tarkov install. All cases end up with the same situation with patcher and my script, where starting the game just displays a few white rectangles and then fades to all white and does nothing else.
Has anyone else running linux ran into similar issues and overcame them? I have looked through the open/resolved issues but nothing seems like it is a match. Thanks!
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