The scenarios I feel like most corporations want to protect against are:
1. Accidental password disclosure, e.g., c/p password to someone who should not know it.
2. Laptop compromised, e.g., with a trojan, keylogger, etc.
3. Laptop physically compromised, e.g., stolen, or opportunistically available (e.g., locked, but sitting on a desk).
It's #2 that's the problem here, and the reason why you want your OTP on a separate device, or hardware designed for it like a Yubikey. In the case of #2, if your OTP secret is on your laptop, and protected by only your laptop password, someone with remote access only needs to log your activity until they have your password, and then they have both your password and OTP.
Were your OTP instead on a separate device, they would also need to compromise that device; with things like a hardware key, this is by design exceedingly difficult, given that it's a separate device designed to never give up the secret, whereas a filesystem can't really tell the difference. That's the point: it should compromising both factors, separately.
But if you're just keeping your OTP secret on disk, and ignoring #2? You're really only covering #1, and a good password manager will make accidental disclosures rather difficult to do anyways, so it seems like little benefit.