In a rational timeline, there’s a clear answer. I submit that we are not currently in a rational timeline.
The fight between Duffy and isaacman keeps NASA on the radar and establishes it for Trump as a valuable object - something that people are willing to fight to have. That perception of value (note - NASA is intrinsically valuable in a rational world, see above) insulates it from Vought. I think the fight over NASA is good for the agency workforce and I hope it continues.
NASA having cabinet-level advocacy is not a bad thing. Transportation is an odd fit but the only other place I could think of it to go would be State given all the international tie-ins. Having someone with the ear of the president is not a bad thing. On the other hand, someone who’s been to space as the administrator is not a bad thing. Someone with actual experience running large organizations is not a bad thing.
Having someone that wants to run the agency like a business is a problem. Having someone that is tied to Musk probably is a problem. Having someone that doesn’t have political capital because they used it all getting the job… that’s a really bad news story.
Honestly, given the choice between two tan white guys with big ears and earnest expressions, I guess I’m actually leaning towards the lumberjack over the credit card processor. See above, we are not in a rational timeline.