I have the 43" Version of the TV! Great value for money IMO. The headphone output from a TV will always reduce the dynamics of the output as it is intended to support headphones which they dont want to damage. Using this output isn't ideal, as you will also have two different volume controls (One for the TV and one for the Bose System if this has its own volume!) So you will definately notice a difference using optical.
Is there no way of going from the TV into the Cinema using Optical? This will send a full dynamic audio through the Optical cable drastically improving the audio. If you let me know the model number of your Cinemate I can look into this for you?
I am not all that familiar with the Bose Cinemate, but I know home cinema. Does the Cinemate unit drive the speakers with a built in amplifier ? So what do the speakers plug into and what do the does that unit plug into?
If you let me know the above, I can assist with advising accordingly.
From what you’ve described and by searching for your system, it sounds like the Sub is active ( do you have to plug this into power?).
In this instance, the external speakers are passive, but your sub contains the amplifier for the other units.
This would be difficult to adjust the sound, unless you adjusted the settings on the TV. Try this and see if the A to D converter makes a difference. You should notice it straight away.
Apologies I meant a Digital to Analogue converter. The only other thing to look into would be a Phono Analogue EQ. This would sit betweenn the DA and Bose system and allow you to sculpt the sound to how you want.