To be clear, a subjugated system without a loyalty marker can simultaneously be a neutral, subjugated, and imperial system for the purposes of missions, objectives, action cards, deployment, and so on. So game effects that apply to "Neutral" systems will also apply to "Subjugated" systems that don't have Rebel loyalty.
It might help to consider "neutral" as a form of loyalty and nothing else. In the same way that a subjugated system with a rebel loyalty marker can simultaneously be a "Rebel Loyal" and "Imperial" system.
The only change I can see this making is to Mon Mothma's "Temporary Alliance" action card, which requires a neutral system. This now works in subjugated systems, whereas it didn't appear to before.
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