Good news: It seems I've managed to solve this problem. There was a serious performance bottleneck in the settings file generation routines that I've identified and fixed completely. The new version 1.8.5 of PixInsight generates its settings file very quickly on all platforms. Even for very large settings files (megabytes), terminating a running PixInsight application does not take more than a couple of seconds, besides the time necessary to remove swap files (which is normally very small unless the amount of generated swap data is huge).
The new version should be ready for release during January. Thank you for your patience.