You do have a point, which could also be extended to say that the property should not be offered if there is no reference mode.
On the other hand, to extend your scenario, if you now set 'IsValueType' to False, the RefMode property will appear and you can set the RefMode property, which will then appear in expanded form. Basically, ExpandRefMode is a property on the ObjectTypeShape element that says 'If the ObjectType I'm associated with does have a RefMode, should the pattern be collapsed?'. This is a moot point if you're currently a value type, but a value type can easily morph into an ObjectType with a ref mode.
For kicks, enter 'A has B()' in the Fact Editor (or 'A has/is of B()' in the new fact editor). Now select the value type role and a uniqueness constraint. Select the new constraint and set its IsPreferredIdentifier property True. If you select A, you'll see that ExpandRefMode is now true.
-Matt