For some reason, the one with the cap tube is pushing out a lower temperature, about 1 or 2 degrees. I have subcooled liquid going to the TEV, about 6K subcool, and a head of 12 Bar, which I've created using a variable condenser fan. The low pressure is steady at about 4.5 Bar.

The other unit runs at 14 Bar, and has a return of 5 Bar. The condenser fan is running faster. I think it has more refrigerant in, but only slightly.

So what do you think the reason for the difference could be?
You have somewhat overcharged your cap tube system as compared to your TEV system. Thus, you are stacking liquid in the condenser providing it more opportunity to become subcooled. This also explains the higher discharge pressure.

The TEV system likely has less refrigerant in it, but you are maintaining a somewhat controlled discharge pressure by diminishing the air over the coil with your fan control. You are not backing liquid up into the condenser, thus you have less subcooling.
For some reason, the one with the cap tube is pushing out a lower temperature, about 1 or 2 degrees.
Are you saying that the cap tube system is providing a cooler air temperature? It is entirely possible. You have a lower suction pressure with the TEV system, so I would expect that you have a higher superheat, all other things considered equal.

The one measurement you have failed to share is the superheats between the two systems. I suspect you have room to decrease the superheat with the TEV by making a minor adjustment to it... trusting that you have a 6 K subcooling.