3.22 mentions 'package' and 'components' and 'should'. This does not state that any particular component has to be used.
The appropriate standard is satisfied by compliance with 3.21 through the built-in safety devices.
As you say, the 2 port valve is there so you can tick a couple of boxes.
You are applying an innovative interpretation to avoid admitting that you were mistaken.
The word “should “ is used in 3.22, which is in the section of the G3 document headed ‘G3: Hot Water Supply and Systems: Guidance’. My understanding of 3.22 is that you should adhere to it’s recommendations in order to ensure you comply with the preceding section, headed ‘Hot Water Supply and Systems: The Requirement: G3’.
The probable reason why the Regulations require the use of the 2-port valve supplied, and leave no room for the discretion of a domestic plumber to select a suitable control valve, is because there are some 3-port valve types which are not suitable for this application. Rotary shoe 3-port valves suffer some leakage through the closed-off port; plug type 3-port valves are mostly only suitable for installation as mixing valves, not as diverting valves and should be fitted in the return. The installation of an appropriate 3-port valve does not ensure that any future replacement will be identical or equally suitable.
The 2-port valve supplied with unvented cylinder package has been selected by the manufacturer and is suitable for the recommended temperatures and pressures. Any other controls (say a modulating valve) should be fitted in addition.