Lily will actually be affected if she continues to wear the Stealth Boy prototype. With this mod, the choice at the end of the quest is now whether you will sacrifice Lily for the good of Jacobstown.
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Contrary to what Doctor Henry says in the game, Lily is not actually affected by wearing the Stealth Boy MK II, and it has no impact on her endslides. There's no reason not to make Lily wear a dangerous prototype, as it helps you get the best ending for Jacobstown.
With this mod, the choice at the end of the quest is now whether you will sacrifice Lily for the good of Jacobstown.
If you decide to have Lily continue using the Stealth Boy prototype, the bonuses to the Stealth Girl perk are buffed. Stealth Boys will last longer, and sneak attack critical hits deal 15% damage instead of 10%.
The downside is that Lily's damage threshold is reduced to represent the damage to her health, and the endslide for Lily's death will play. If you have FPGE installed, Lily will be unavailable after the Second Battle for Hoover Dam.
This mod also forwards changes for YUP, including the perk description for Stealth Girl.