Can Private Pilot training, funded by employer, count as company hours?
No law against this. Nor is there any restriction on who pays for your flight training. You are referencing something which applies to your privileges as a student pilot. You may not act as Pilot In Command (PIC) for compensation or hire, nor carry passengers or cargo for compensation or hire - see §61.89. Having an employer pay for your flight training cannot be viewed this way. Again, these regulations are only applicable to time as PIC, so, as a student, this would be only solo flight time.
Now, if the employer attempts to have you perform flight duties in the furtherance of their business while you are a student pilot, i.e. they asked you to ferry an airplane for them somewhere, or perform some other task which is not related to your flight training, that does violate the law. However, the employer only paying for you to undergo flight training is not a violation of federal law.