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The above issues won't occur if you already have an IFF locked in. Running no IFF at all won't be possible, as every ID will rephack you to its default affiliation.
Most IDs will also have maximum rep thresholds set so you can't set an IFF, except for the faction that corresponds with your ID.
This means under the proposed system, the only way your hypothetical freelancer ends up with an LN or LR IFF is if you've specifically used droprep to clear your IFF and lock in the next ellligible faction.