Methods: Does failing at intermolecular properties mean the same for intramolecular properties? Let us consider the following:

1.) Method X fails at describing intermolecular non-covalent interactions.

2.) Method X excels at describing molecules of type Y.

3.) Method X ___?___ at describing molecules of type Y_1 containing intramolecular non-covalent interactions.

Is there an existing general consensus on number 3? I haven't found an example in the literature yet which would highlight a clear answer to this.

EDIT for clarification:

Example 1: An non-covalent intermolecular interaction would be the interaction of two stacked benzene molecules.

Example 2: A molecule of type Y could be like an amino acid. This molecule has well defined, strong covalent bonds.

Example 3: An organic molecule with a non-covalent interaction occurring between two functional groups.

So... regarding #3, would we expect the method to do well at characterizing a molecule in Example 3, would we expect the method to fail (as it did in Example 1) or is there no general consensus on the matter which is essentially the same as saying, "Just have to try it and see!"?
I think the distinction that you are trying to draw is (as you have hinted) better expressed in terms of covalent and noncovalent interactions, rather than inter- versus intramolecular interactions. A technique that fails to correctly describe noncovalent interactions will fail whether or not these interactions are between two moieties on the same molecule, or on different molecules. The usefulness of a technique that fails noncovalent interactions is contingent on whether or not those interactions are significant to the particular properties of a molecule that you are investigating.