I'm afraid I can't offer you any guidance as to the chronology of "Secrets of the Omnitrix" in the series as whole but I can say from personal experience that it doesn't spoil anything for later viewing of the show. I personally think it stands alone and I reckon it was deliberately designed as such. I watched it before seeing a full episode of the series and have only now started watching the series beginning with season 1. As far as I can see/guess it hasn't spoiled anything.
Of course I can still understand that you want to watch the entire story in chronological sequence. Sorry I couldn't be more help.
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