They might try, but the combination of chapels, shrines and Icons to the Star Child probably means it's impossible to strip out all of it. Besides, we're kind of specifically giving it to the Iconoclasts within the Duchy. It's possible they in particular are more receptive to the notion. I bet the players in Zandtquest get the option and go "huh. Maybe let's see if it does help against the nurgle bullshit."
I don't see how? We can build religious icons that won't fit through the doors of the shrines, but that just means that they'll have to break them up before throwing them in the trash.
That's why it has a Large On-Board Manufactory and doesn't shoot projectile weapons. It's completely self-sufficient. In fact it probably produces enough surplus parts to do maintenance on all of the other ships we're sending along, which would also be white elephants without The Gift of Guiding Light
The Gift is most certainly not entirely self-sufficient. The Large On-Board Manufactory can build
nearly any supply part. When one of the parts it can't build breaks, then the Gift is up a bit of a creek.
However that's not the main issue. The Free Duchy might not be able to manufacture the necessary parts now, but it shouldn't be too difficult to fix that. They'll be pricier than the standard ones, due to economies of scale, but it's quite manageable (making your assertion that the other ships will be white elephants without the Gift absurd), but it can be done.
The issue the Gift poses is that whenever the Free Duchy wants to park it, be it for maintenance or to grant crews shore leave. they'll be stuck with a rather unpleasant choice. They could expand their void infrastructure in that specific area, at significant time and expense for a single ship. Alternatively, they could set up an improvised setup, likely involving significant amounts of shuttles, which would render said infrastructure partially or entirely useless in that specific situation, also leading to significant additional time and expense compared to a conventional ship.
Forced to? They asked. We delivered. In fact, this would be massive over-delivery, and to the faction in the duchy that is friendly to us. It's both a declaration that we're good friends to have and that they better not mess with us because there's more where that came from.
It's only over-delivery if they'd prefer a massive battleship they almost certainly don't have the doctrine to use properly instead of an equivalent amount of resources spent on ships they have experience in using. At that point it stops being a gift and becomes us taking advantage of their desperation to perform a juvenile dominance display.
Moreover, we will be placing them in an awkward position that they most certainly didn't ask for and it's extremely likely they don't want. They can replace their current flagship with ours, angering everyone who isn't an Iconoclast and a few who are. Alternatively, they could choose not to do so, a decision that is both tactically unsound and likely to piss us off.
If anybody has any problems with the Gift of Guiding Light I won't be offended if you make a variant of the plan with a different design there, but I do believe that as it stands it is a useful conversion tool.
I'd love to, but I don't have the time or experience with the ship building system to do so before the moratorium expires.