Hi Kurt,
I’m afraid your information may be out of date. Windows totally uses the SKI/AKI, and in recent versions of Windows 10, explicitly limits the number of unique SKI/key pairs you can have (that is, shared SKIs with unique keys), as a way of limiting the number of signatures considered during path building. Windows does this before and independent of the subject/issuer name matching.
Other products, such as Adobe, are notable in going further, in which SKI/AKI fully replaces name chaining in some products.
Are these good ideas? In Microsoft’s case, the right intent is there, even if the execution is surprising. NSS has its own similar weird quirks (like issuer and serialNumber uniqueness, even from separate certificate hierarchies), so I’m certainly not trying to cast aspersions here.
The primary reason PKI designers prefer the SHA-1 approach over the unique approach is that it allows client implementations to synthesize the SKI for issuers in the event the AKI is present in the issued cert, which is a scenario that used to be far more prevalent. The unique approach also has the downside of causing clients to prefer certain paths, which can make mid-stream PKI transitions more difficult (replacing an old issuing intermediate with a new one).
However, as you noted, despite these quirks, most clients will not be security affected, and as Andrew noted, it’s not the same risk that the prohibition in policy is defending against (similar to the reason with OCSP ResponderIDs)