Having a TOTP secret would protect against theft of credentials in transit. The TOTP is only valid once, so that credential exchange is only valid once. They wouldn't be able to create any additional login sessions with the information they've attacked. However, there's a good chance if they could see that they might also be able to see a lot of other information you're exchanging with that service.

It creates a race condition in transit - if they can use the code before you, then they win. I can intercept at the network level, but also via phishing attacks - there is no domain challenge or verification in TOTP.

I know having someone malicious get into your account multiple times vs once is likely worse, but its hard to quantify how much worse it is - and of course using that one login to change your 2FA setup would make them equivalently bad.

Not quite exactly "equivalently bad", since a user is more likely to notice a 2FA setup change than they are a phishing site's login error and then everything working as usual, but yeah, perhaps it's splitting hairs at that point.

which is why I'm wary of using my password manager for OTP, and use a separate one. Not sure if it's too paranoid, but it doesn't make sense to me to keep the 2 in the same place.

There appear to be two points being conflated — 1/ 2FA via secrets stored on a separate device from your primary device with a PM provide more security than those stored on one device, and 2/ once you use a PM with unique password for every site, much of what OTP helps with for is already mitigated.

Both seem true, and what to do to protect yourself more depends on what kinds of attacks you're interested in stopping and at what costs. Personally, PM + U2F seems the highest-security, fastest-UI, easiest-UX by far — https://cloud.google.com/security-key/

If you're using 1p password for storing your passwords, then yeah, it would make sense to use something else for your TOTP.