i understand why you want to implement the rebake NPCs. your listed reasons are sound, especially irt how rough a computerized GM would be and how some NPC features are duds. i'm quite a fan of the rebakes myself, having fielded them on many occasions over the vanilla roster just because i like em better
that said, i would be disappointed to see third party materials used in LT. it was my expectation that this game would be as close to a faithful adaptation to vanilla Lancer as possible. i get that some things inevitably must be changed for the sake of swapping mediums; its unavoidable. no big shakes. but i didnt expect a change quite this large. the rebake NPCs are indeed designed to honor the spirit of their vanilla iterations, but they still differ quite significantly in terms of mechanics and i think those differences might be understated here (even if i think they are differences for the better!)
its a tough one. i absolutely think the game would be easier to make with the rebake. but ultimately i fell in love with Lancer as-is, warts and all. i was looking forward to having something loyal to the original experience that i could pick up between campaigns when i got the itch. i would still do that even if LT ends up using the rebakes, naturally, but it wouldnt be the same
you should of course make the decision thats best for you and your project, just adding my two cents. this game is a miracle and im excited to play the final version no matter what direction you take it!