Running the game on Windows with the -debugoutput command line argument yields these first few lines:
Create Error Form
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* YoYo Games Runner v1.0(999)[r32908] *
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RunnerLoadGame: D:\Program Files (x86)\Steam\steamapps\common\Unworthy\data.win
#########################################################################
####!!!!$$$$$$ pwd - D:\Program Files (x86)\Steam\steamapps\common\Unworthy\
#########################################################################
RunnerLoadGame() - D:\Program Files (x86)\Steam\steamapps\common\Unworthy\data.win
YYG Game launching. Game file: D:\Program Files (x86)\Steam\steamapps\common\Unworthy\data.win
Checking if INIFile exists at D:\Program Files (x86)\Steam\steamapps\common\Unworthy/options.ini
Reading File D:\Program Files (x86)\Steam\steamapps\common\Unworthy\data.win
[...]
Ryuku's Linux runner at least is v1.3. Not sure about the Windows version.
EDIT: It turns out this is not enough, as Ryuku's runner version on Windows is identical, but does not feature the bug.