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If you are using his script there, then it would be safe to say that you are now testing GPS time. To make your test complete and cover the case that you were using GPS time prior* (cos its built into the boot file naturally), thus meaning you compared nothing. I recommend you test setting the time manually in the menu, and seeing if you get better or worse or same results with that. Make sure to remove the custom boot code you installed. The downside to this method is if you use the 'Turn off' Feature, then your time is lost. Good Luck!
After a few days' trial, it seems to me that the watch still gains almost 2 seconds a day. Because the new script is in custom boot, perhaps I'm missing a boot action to activate it? All I'm doing after the GPS fix and uploading the custom boot is pressing BTN3. (A more serious reboot seems to replace the time with a default time.) I may be missing something.
Would the script be more likely to work as desired (and not be subject to nullification by a novice) if embedded into the watch's own script?