Welcome to the forums. You posed a question in the review, and I'll give you an answer in spoiler tags:
During the training missions, the Theseus is actually testing CNP on a single viper - they explicitly say the CNP is not yet installed on the Theseus. During training 2 debriefing, it's said the Theseus is being sent on a long patrol (several months worth) and at this rate they'll be the last ship that actually gets the CNP upgrade. The attack on the colonies actually happens as they're finishing their patrol duty. It's just one of those categories that needs to be handled in a subtle way, or it just feels forced in.