Great question, we need to document this. For Linux you should be able to set a system-wide value for this by creating:
/etc/xdg/RStudio/desktop.ini
containing:
[General]
desktop.renderingEngine=software
Make sure the file is readable by all users. One catch, users can still change the setting and their per-user setting will override this system-wide setting.
Gory details:
This particular setting is persisted via the Qt framework's QSettings class, with the IniFormat on Linux and Windows (and the binary format on Mac). The location of this system-wide file is based on the XDG_CONFIG_DIRS environment variable (the default value being /etc/xdg).
Even more details here: https://doc.qt.io/qt-5/qsettings.html