Do you think the situation is different in more specialized niches (i.e. would I be able to reasonably compete with a CS grad for a job at a biotech firm?)
Yes, but honestly it really depends on what you want to do.
As an example, I'm currently starting to hire for a small tech company in the life-sciences space. A candidate with real lab experience would be significant differentiator though its not super necessary for the position. On top of that having a PhD is a strong signal in favor of a candidate. That being said, given my position I would likely just pick a more-technically competent candidate if one is available, though that won't be the case everywhere you look.
The closer you get to the bigger biotechs, I'd imagine the more your PhD will be worth in terms of differentiating you as well. If you need to talk to scientists on a daily basis, you'll need to know how speak the same language, and thats not something you can get from a bootcamp.
My best advice would be to learn a breadth of technical skills and to start honing the ones that make sense for you personally. Don't let any tell you "you need to focus on X to be successful in biotech." There is a lot of innovation going on in the space right now, and if you look in the right places I'm sure you'll find that niche that makes sense for you.
I did something similar to what you describe ten years ago, finishing a chem phd and pivoting to data science (back when data science was still the coolest job around)
My first job was at a big consulting outfit, they hired me no questions asked. I did do ~ 2 years of high-volume DFT calculations on a computing cluster during the phd. Ensure you have some edge that makes it believable that you can operate a linux box/do scripting, and you'll be fine.
Maybe the market is different now, but if I'm hiring people right now, having completed a STEM-ish PhD seems to signal intelligence and perseverance. Just don't come off as an academic know-it-all. Noone cares if you're right in industry, your shit just has to be delivered on time.
If you want to go biotech and software, I'd say try to pivot into a data scientist position