The issue ended up being the UpgradeCode. We are using uuidgen to generate the UpgradeCode from the product name (org.openrgb.openrgb) but for the plugins the product name contained spaces (org.openrgb.openrgb effects plugin) and it seems like it was ignoring everything after the space and generating the same UUID. I noticed in an install log that RemoveExistingProducts was uninstalling the plugin during OpenRGB installation and tracked it down to the identical UpgradeCodes. Fixing the product name to remove the spaces fixed UUID generation and now the packages don't uninstall each other.