The bias is set at 22mA and the plate voltage is 439V
Isn't that on the cold side?
No, that's dead-typical for a blackface Princeton.
440v * 0.022A = 9.68w
9.68w / 12w = 80.7% dissipation
Yes, you might subtract screen current from cathode current (but these amps don't have 1Ω resistors stock, so he may be using the OT shunt method of measuring plate current). Yes, you might use 14w instead of 12w as your plate dissipation number. However, I know when I had my old Princeton serviced by a competent "guru" (in the days before I knew much of anything), he biased it to 22mA at idle.
When I also turn the bass control to zero and the treble is to zero I hear a thin sounding amp with some presence/treble on the notes. :(:(
Ummm... don't tun the tone controls to zero?

Google "Duncan Tone Stack Calculator". Download it. Select the "Fender" tab (which is selected by default when you launch the program). Set the "Mid" slider to about 6.8. Set the "Treble" and "Bass" sliders to zero. Output with be reduced as shown on the graph but will not be off in any setting. The 6.8 setting of "Mid" mimics the 6.8kΩ resistor you have in your Princeton's tone stack.
I think you you may be perceiving things as problems which are not problems. Without hearing both amps & tinkering them in person, it is impossible to understand what difference you heard between them, much less what might be causing such a difference.
I'm sympathetic to your position because when I got my first tube amp (a '67 Princeton Reverb), I tinkered with almost everything in it, thinking I make it sound "better". I started with an amp that sounded like a Fender Princeton and ended up with an amp that sounded like a Fender Princeton.
If there's not an obvious problem (redplating tubes, crackling output, huge hiss, hum louder than the guitar), I'd humble recommend letting the amp be what it is. Which after all is a pretty cool old Fender...