While I have made this suggestion in the replies of another thread, I've been thinking about it and realized this fits even better than I realized at the time. While the industry tree does have some combat potential, it's also the only tree there for players who want to roleplay a merchant or explorer instead of a mercenary type of character. It does have some combat bonuses between the piloted ship skills and top tier skills, but that's not the focus of the tree. This is why I think hull restoration giving CR clashes a little bit with other aspects of the tree, because the bonus is almost exclusively useful for combat.
Ultimately starsector's strongest selling point is its combat, and even if you aren't focused on combat it is going to be part of your playthrough one way or another. It's fair to say that hull restoration is working fine as is, and it doesn't *need* to be changed, but consider if instead of CR it gave you a 3rd s-mod. This is still very useful for combat focused players, but is also useful for a non-combat approach due to s-mods letting you go over the normal limit for logistics hullmods. At first glance it seems like a great idea! It's thematically fitting for the industry tree and is flexible enough to be useful for both combat focused and non-combat focused playstyles.
Also, I believe part of the intention with the current design is that industry is meant to allow you to field a "wider" fleet that can afford to take more losses. With derelict operations this is obvious, and with hull restoration it's a bit less obvious, but you'll notice the CR bonus does not have a dp cap the way crew training does. This allows you to have ships over the normal 240 dp limit with full CR, and the expectation is that you're going to lose some ships but that's okay because you have replacements you can send and the d-mods will be repaired for free anyways. I understand this, but my issue is that derelict ops is already appealing for the "quantity" mindset, whereas hull restoration cleaning up your hulls appeals to a more "quality" oriented mindset.
This does leave an open question about what to do with botb, but if I get started on that it will devolve into rambling about reworking the whole skill tree and I'd rather keep this suggestion concise.