When doing manual calibration you are really only using ColourSpace to show the values being read.
To get the Target/Actual values to correctly define how close, or not, you are when making adjustments, you need to set the Luma Target Nits (Min/Max) in Settings to the desired values.
The variation of the Actual values to the Target values are defined by those, in combination with the Target ColourSpace.
In most instances the Min/Max values are the TVs measured Black/White values, after you set them to the approx. wanted values, and can be automatically updated every time black or white is measured, by selecting the '^' tick box in Settings.
Then, when measuring the patches, the patches must match the TV's expect input values.
If they do not match, the results will never be right.
This is critical.
It then a question of just getting the correct readings for each patch while taking manual measurements, and adjusting the TVs CMS controls.
I would not use probe matching initially, until you have things close - use it after to verify and make small corrections.
Using things like Chroma Only for the RGB Bars is a user preference, as they Luma bar always show that anyway.
Some users like to have Luma in the RGB bars calculation, some don't...
But yes, it is very likely that changing one level on the TVs CMS will affect other levels, as the controls tend to work over a 'range', and not a single level.
But all of this is why we focus on LUT based calibration.
Manual TV calibration really is extremely limited in the level of accuracy it can attain.
And many TVs have very poor controls.
An external LUT box, or home cinema system is a far better bet.
(Or a TV with internal LUT capability... if you can put up with LG TVs...)
Mob Boss at Light Illusion