The problem here isn't so much with transparency as with delegating cryptography to non-cryptographers (or, for that matter, trusting that other vendors have had cryptographers review their designs). Based on the track record not only of open source cryptography but also of internal review of closed-source cryptography (that is: closed source software reviewed by the vendor that wrote it), having access to designs and code is of marginal importance. Crypto bugs of comparable severity have lived for many, many years in these systems.
What you actually want is an assurance that no link in the security chain of a system protected by cryptography depends on a cryptographic capability had hasn't been formally assessed. Ideally, you want the specific name of the person who assessed it. For instance: Intel's SGX setup has been audited by third parties and was also designed and in some sense overseen by Shay Gueron. You will never see any of that underlying code, but you would probably be crazy to trust an comparably ambitious un-vouched cryptographic enclave more than SGX. Similar story with Amazon and KMS (again: Shay Gueron, but also in-house crypto experts at AWS).
If anything, this story illustrates how weak an obstacle closed source really is. This is an academic project, and they tore up something like 8 different drives and game-overed most of them.
Of course, I agree with the broader point that Microsoft shouldn't have trusted hardware cryptographic capabilities they clearly knew nothing about (Microsoft also has sharp crypto people, all of whom would have barfed all over any of these designs).